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Question 1

Compare the amount of time that bacteria have been on earth to the amount of time that macroscopic life has been on earth. What evidence is there for the presence of bacteria during the earliest days of life on earth?

Answer 1

It’s said that the first type of Photosynthetic bacteria was discovered from fossils in rocks dating from at least the Devonian period 3.5 billion years ago. comparing that to macroscopic organisms with signs of life 2 billion years ago, leaving behind carbon molecules in stromatolites that could only be described as living organisms.

Question 2

Humans use microbes for all kinds of purposes. Which microbes contributed to the oxygen revolution event > 2 billion years ago?

Answer 2

The microbes contributed to the oxygen revolution event was cyanobacteria. They conducted photo-synthesizers.
They used water and sun’s energy to make food and release oxygen to atmosphere, making aerobic respiration possible.

Question 3

Humans use microbes for all kinds of purposes. How do we use microbes for fermentation to produce food?

Answer 3

Some examples of the use of microbes and fermentation in food production are:
- Saccharomyces cerevisiae

After the works of Louis Pasteur and the understanding of a microbiological factor for certain foods, Great Britain introduces growing vats for this fungus, S. cerevisiae, in 1879, allowing for widespread commodification of bread, beer, wine, and various alcoholic beverages.

• Genus Lactobacillus
  First isolated by Austrian pediatrician Dr. Ernst Moro in 1900, this genus of anaerobic bacteria has numerous species that are used in the production of lactic-acid fermented foods such as yogurt, kimchi, and sauerkraut.

Question 4

Humans use microbes for all kinds of purposes. How do we take advantage of microbes in drug (antibiotics) production?

Answer 4

We have taken many approaches to utilize microbes in drug production. The prime example would be the discovery of penicillin fungi, which produced a chemical that essentially inhibits peptidoglycan production, making the bacteria fragile and easy to kill. In addition, most of our antibiotics have been discovered in bacteria such as the genus Streptomyces. These bacterias need antibiotics to increase their competitiveness in nature by killing off other bacteria. This website has a table that describes what antibiotics came from and which microbe.

Question 5

Humans use microbes for all kinds of purposes. What is bioremediation?

Answer 5

Bioremediation broadly refers to any process wherein a biological system, living or dead, is employed for degrading environmental pollutants from air, water, soil, flue gasses, industrial effluents etc., in natural or artificial settings.

Question 6

What are microbes causing human diseases called? People once believed that all microbial diseases would be controlled by the 21st century. Yet - we continue to identify new diseases. Why does this happen?

Answer 6

They are called pathogens, pathogens are ever evolving and with the invention of mass global travel, its become more likely for certain pathogens that didn’t effect humans would mutate and start becoming a human disease

Question 7

What period was considered ‘the golden age of microbiology’? What were the contributions of Louis Pasteur?

Answer 7

The golden age of microbiology was around the late 1800s and the early 1900s. Pasteur contributed with fermentation and pasteurization(the name given after him). He developed a theory called the “Germ Theory “ which stated that other pathogens caused diseases and also caused their infection.

Question 8

What period was considered ‘the golden age of microbiology’? What were the contributions of Robert Koch?

Answer 8

The Golden Age of Microbiology was around the mid-to-late 1800s. Koch was known for studying anthrax, cholera and tuberculosis, but he was best known for establishing the ‘Koch postulate,’ which led to the discovery of specific microbes that could cause specific diseases.

Question 9

Do you know the difference between taxonomy and phylogeny?

Answer 9

The key difference is sort of easy to spot when you examine the word phylogeny. As it has the word gene embedded into it, this is because phylogeny is based off genetic material revealed through DNA and RNA sequencing. Meaning Phylogeny has hard evidence, even if we forget everything about phylogeny today, in a couple years once rediscovered, all the learned material would be exactly the same as before the information was lost.

Taxonomy, although is mostly based off phylogeny now, was originally an anecdotal system of classifying animals based off physical similarities, meaning at least at the beginning it was not reliable information.

Question 10

Who invented binomial nomenclature? And do you know how to write species names properly?

Answer 10

Carolus Linnaeus invented binomial nomenclature. Binomial nomenclature is a two word name to organize and characterize organisms.
The genus (first name) first letter is always capitalized and the specific epithet (second name) first letter is lowercase
both parts must be lined or italicized.

Question 11

The following is the genus and species name of a bacterium. Apply correct binomial nomenclature! Briefly explain what you changed.
escherichia coli

Answer 11

Escherichia coli
Italics, genus capitalized

Question 12

The following is the genus and species name of a bacterium. Apply correct binomial nomenclature! Briefly explain what you changed.
Bacillus Subtilis

Answer 12

Bacillus subtilis
Italics, epithet lowercase

Question 13

The following is the genus and species name of a bacterium. Apply correct binomial nomenclature! Briefly explain what you changed.
staphylococcus Aureus

Answer 13

Staphylococcus aureus
Italics, genus capital, epithet lowercase

Question 14

What are the three domains of life? What molecule did Carl Woese use to divide all of life up into these three domains?

Answer 14

Domain Archaea: Domain archaea contains organisms which have prokaryotic cells. They lack nuclear membranes. They contain RNA markers from bacterial cells. Archaea are considered the oldest species of organisms on Earth and the term archaea is taken from the ancient Greek word which means ancient things. They have the ability to survive in extreme and harsh environments because of their specialized cell wall. The cell wall of archaea lacks peptidoglycan.
Domain Bacteria: Domain bacteria also consist of prokaryotic cells. They are also called eubacteria or true bacteria. Their cell wall is made up of peptidoglycan. Their cell membrane is made by an ester linkage formation between unbranched fatty acid chains and glycerol.
Domain Eukarya: The domain Eukarya contains organisms that have eukaryotic cells with membrane-bound nuclei. They may have cell walls present in them. The cell wall present in them is made up of cellulose and chitin. They do not have peptidoglycans on their cell wall.
Carl Woese used ribosomal RNA

Question 15

Which domain (bacteria or archaea) is most closely related to Eukaryotic organisms?

Answer 15

Archaea is most closely related to Eukaryotic organisms. American Biologist Carl Worse and George Fox collaborated on creating a “genetics based tree of life” which explores the similarities and differences in organisms. The tree has branches and subbranches that represent the 3 different level of kingdoms(Archaea, Bacteria and Eukarya) and organisms in each kingdom. In this tree it shows a closer relationship between archaea and eukarya.

Question 16

Do you know the size range of prokaryotes, and whether they can be seen by naked eyes, light microscopes vs. electron microscopes?

Answer 16

Detection limit: naked eyes (~200 um)
light microscope is needed to see bacteria within 0.2 micrometers vs. electron microscope that is required to see DNA, small proteins and macromolecules and is within 0.1 micrometers.
Prokaryotes have a typical diameter around 1 micrometer.

Question 17

Do you know the size range of eukaryotes, and whether they can be seen by naked eyes, light microscopes vs. electron microscopes?

Answer 17

Detection limit: naked eyes (~200 um)
10–100 μm
Light and electron microscope

Question 18

Do you know the size range of viruses, and whether they can be seen by naked eyes, light microscopes vs. electron microscopes?

Answer 18

Detection limit: naked eyes (~200 um)
10nm
Electron microscope

Question 19

When light hits an object, what are its possible fates? List all three and briefly describe.

Answer 19

It can be absorbed and disappear
It can be reflected, this is the color our eyes perceive
It can be transmitted if the subject is transparent
White color reflects all wavelengths
Black color absorbs all wavelengths

Question 20

Do you know the relationships between wavelength, frequency and energy status for different light waves?

Answer 20

The relationship between wavelength, frequency, and energy of a light wave is described by the equation: E = hf = hc/λ.

Where: E is the energy of the photon

h is Planck’s constant

f is the frequency of the wave

c is the speed of light

λ is the wavelength of the wave

This equation shows that as the frequency of a wave increases, the energy of a photon increases, and as the wavelength of a wave decreases, the energy of a photon decreases. In other words, short-wavelength light (such as ultraviolet or x-rays) has more energy per photon than long-wavelength light (such as infrared or radio waves).

Question 21

What is the electromagnetic spectrum (EMS)? Do you know the wavelength range of visible light?

Answer 21

The electromagnetic spectrum is a range or “spectrum” of electromagnetic energy or radiation which is based upon both wavelength and frequency. The visible light range, in terms of wavelength, is roughly 400 to 700 nm, which spans from “high energy” violet to “low energy” red.

Question 22

What is the electromagnetic spectrum (EMS)? Do you know the wavelength range of UV light? Do they have more or less energy than visible light?

Answer 22

100-400 nm
Visible light is 400 to 700nm
UV light has more energy, It is one step above in terms of having higher frequency and shorter wavelengths compared to visible light

Question 23

Do you know if X-ray have more or less energy than visible light? Use their wavelength and frequency to explain.

Answer 23

X-ray tends to have more energy than Visible light because it’s wavelength appears more shorter and with shorter wavelengths are much more faster. It could go through most objects such as the human body. Compared to visible light it has shorter wavelengths and contains less energy.

Question 24

Do you know if microwaves have more or less energy than visible light? Use their wavelength and frequency to explain.

Answer 24

Microwaves have less energy than visible light so they have lower frequency and bigger wavelengths

Question 25

Do you know how to calculate the total magnification of a compound light microscope? Use an example to illustrate.

Answer 25

While optical lenses are typically a standard 10 times, objective lenses tend to vary more and come in sizes of 4, 10, 40, or 100 times magnification. With current technology, the maximum known magnification for light microscopes is 1000x, which is more than suitable for the most complex applications.

Question 26

The detection limit of each microscope is set by its resolution, what is it?

Answer 26

the resolution of objects: the ability to tell that two separate points or objects are separate. A low-resolution image appears fuzzy, whereas a high-resolution image appears sharp.
Two factors affect resolution.
The first is wavelength. Shorter wavelengths are able to resolve smaller objects; thus, an electron microscope has a much higher resolution than a light microscope, since it uses an electron beam with a very short wavelength, as opposed to the long-wavelength visible light used by a light microscope.
The second factor that affects resolution is numerical aperture, which is a measure of a lens’s ability to gather light. The higher the numerical aperture, the better the resolution

Question 27

What is contrast, and how can we enhance it for easier detection?

Answer 27

Contrast is the difference in light intensity between the object your are looking at and its background. You can enhance contrast by adjusting the light intensity and condenser when using a microscope or by subjecting your slides to different stains.

Question 28

Can you explain the difference between brightfield vs. darkfield microscopy? What is darkfield known to be better at?

Answer 28

A brightfield microscope is the most commonly used type of microscope. It is a compound microscope that has two or more lenses that produces a dark image on a bright background. A brightfield microscope creates an image by directing light from the illuminator at the specimen. This light is differentially transmitted, absorbed, reflected, or refracted by different structures. In order to increase contrast and resolution, stains are often added to the specimen so it can be seen clearly through a brightfield microscope.

A darkfield microscope is a brightfield microscope that has a small but significant modification to the condenser. It can often create high-contrast, high-resolution images of specimens without the use of stains. Darkfield microscopes are known to be better at viewing live specimens that can often be compromised or killed by stains.

Question 29

Can you explain the difference between brightfield vs. phase-contrast microscopy? What is phase-contrast known to be better at?

Answer 29

Brightfield produces a dark image on a bright background, while Phase-contrast microscopes add a lot more complexity through light refraction and phase interference which produces greater contrast. It enables the viewer to see structures that might be invisible when seen through a typical brightfield microscope. Phase contrast microscopy is better at viewing granular details of living specimens because it can heighten contrast without staining or otherwise killing the specimen.

I’m not totally sure I understand the physics of how the light is refracted and how that creates more contrast. If someone is able to explain in more simple terms that would be much appreciated!

Question 30

Electron microscopes can detect much smaller objects than light microscopes can. Can you use wavelengths and resolution calculation to explain this phenomenon?

Answer 30

Reason for electron microscopes being able to detect smaller objects than light microscopes is because electrons have shorter wavelength than photons. Therefore electron microscope could be used to observe biological and inorganic specimen. It’s beams of electrons are used to illuminate specimen, mainly due it’s wavelengths being much shorter resulting with much higher power compared to light microscope.

Question 31

Compare scanning EM (SEM) and transmission EM (TEM) to see what they are designed to detect.

Answer 31

A scanning EM (SEM) - scanning electron machine is a type of electron microscope that produces images of a sample by scanning the surface with a focused beam of electrons. The atoms of the sample then interact with the electrons, producing a great depth of focus. This bigger viewpoint can allow the viewer to image the whole specimen and things that would display patterns and the overall shape.

The transmission electron microscope (TEM) can view thin slices of a specimen. It’s used to image the interior of cells, the organization of molecules in a virus, and the structure of protein molecules.

Question 32

A patient walks into the clinic with a set of signs and symptoms. Use the five I’s to describe how you would take the sample and use it to identify the pathogen. (Note: this question can be answered by multiple students if each student covers a different disease. Use the typical symptoms for a specific disease to start with.)

Answer 32

The 5 I’s are
Inoculation - to introduce a small amount of bacteria(the Inoculum) into fresh culture media which may or may not have nutrients to support bacterial growth

Incubation - inoculated culture is placed in a temperature controlled incubator to stimulate human body temp of 37 degrees C

Isolation - To give the patient the right medication to treat their infection, it is often necessary to isolate bacteria from a mixed culture to produce a pure culture of one bacterium. to getting a pure culture is the ability to get single colonies, which will only develop if the plating cell density is low enough. So all the isolating techniques include some form of serial dilution, are to get to the right cell density that can produce isolated colonies.

Inspection - Inspection simply means to examine the microorganisms, either macroscopically observing the growth patterns in media and colony morphology, or microscopically observing the staining results for cell morphology (Figure 9). Both the colony morphology (color, texture, size, etc. of the colonies) and the cell morphology (shape, arrangement, etc. of the cells under microscope) hold clues to the identification of the microbes.

Identification - Identification of the microorganism to the species level is the goal of most clinical microbiology labs. Identification is based on many criteria, including morphological data that we just talked about, and other biochemical, immunologic and genetic tests. Morphology alone is rarely enough. For example, you observe that the colonies of your bacteria on an agar plate is circular, with a smooth margin and white color. These colonies could be E. coli, Enterococcus fecium, Staphylococcus epidermidis

Question 33

Describe the differences between pure culture, mixed culture and contaminated culture.

Answer 33

A pure culture is a bacterial culture of only one strain or species.

Mixed culture means at least two different species of bacteria are in the culture, but these species are known and intentionally incubated.

Contaminated culture means there are unknown species of bacteria in the culture and were unintentionally incubated.

Question 34

How are complex media different from chemically defined media? Can you tell them apart by looking at the ingredients? Give an example of each.

Answer 34

Chemically defined or synthetic media has only known chemical ingredients. the recipe for the media is known and precise amounts of each chemical are added. The recipes are long since there is an exact amount of each ingredient added. An example is EZ medium.

In comparison, complex media has at least one component that is not chemically defined usually some sort of natural extracts like blood, serum, meat extracts, or infusions. These come from plants animals or yeast. These recipes are much shorter since the natural medium contains many of the necessary nutrients and each ingredient is not added separately. The exact chemical nature of these medias are not known. Examples include nutrient broth, tryptic soy broth, and brain heart infusion.

Question 35

What are general purpose, enriched, selective and differential media? Give some examples of each.

Answer 35

All-purpose media support growth of a large variety of organisms. Examples of all-purpose media is tryptic soy broth (TSB), or tryptic soy agar (TSA).

Enriched media contains growth factors, vitamins, and other essential nutrients to promote the growth of fastidious organisms (organisms that cannot make certain nutrients and require them to be added to the medium). Examples of enrich media are blood agar, which contains blood from sheep, horse or rabbit added to the agar base; and chocolate agar, a modified blood agar.

Selective media inhibit the growth of unwanted microorganisms and support the growth of the organism of interest by supplying nutrients and reducing competition. Example of selective media is MacConkey agar EMB agar, Mannitol Salt agar, MacConkey agar, and Phenylethyl Alcohol (PEA)
MacConkey agar contains bile salts and crystal violet, which interfere with the growth of many gram-positive bacteria and favor the growth of gram-negative bacteria. MacConkey agar is used to identify the Enterobacteriaceae.
Enterobacteriaceae is species reside in the intestine, and are adapted to the presence of bile salts

Differential media make it easy to distinguish colonies of different bacteria by a change in the color of the colonies or the color of the medium. Color changes are the result of end products created by interaction of bacterial enzymes with differential substrates in the medium or, in the case of hemolytic reactions, the lysis of red blood cells in the medium.

Question 36

Why is isolation important? What is the appropriate medium (slant, broth, plate or deep) for isolation? Please explain.

Answer 36

Isolation is important because it can identify the bacteria that is responsible for causing disease. It is also important because it can help prevent the transmission of microorganisms.
A pure agar culture plate is appropriate because it can be used to separate mixtures of bacteria, which allows us to observe colonies.

Question 37

Compare and contrast wet mount, hanging drop and fixed smear preparations for microscopic observations. When is it appropriate to use each method?

Answer 37

The most simple is wet mount, a specimen is placed in a drop of liquid with a cover slip on top. Wet mount is good for viewing live specimens.

Hanging drop is used for viewing cell motility

And fixed smear is as it implies, to fixed your specimen to the slide

Question 38

What are basic vs. acidic dyes? What kinds of staining can we use them for? Give a few examples of each.

Answer 38

If the chromophore is the positively charged ion, the stain is classified as a basic dye, a dye that will be absorbed by the negatively charged cells or organisms being observed, adding color to objects of interest to make them stand out against the background. Examples of basic dyes are methylene blue, crystal violet, malachite green, basic fuchsin, carbolfushsin, and safranin.

If the negative ion is the chromophore, the stain is considered an acidic dye, which is absorbed by the background but not by the cells or organisms in the specimen if negatively charged. Negative staining produces an outline or silhouette of the organisms against a colorful background, but if the specimen is positively charged the dye will penetrate the molecules and structures. Examples of acidic dyes are eosin, acid fuchsin, rose bengal, and congo red.

Question 39

What are simple vs. differential stains? Give some examples of each.

Answer 39

Simple stain- requires one single dye and can reveal size and shape

(Ex) Crystal violet, methylene blue and safranin.

Differential stain- two dyes are needed. Requires a primary and counterstain and helps to see cell structure.

(Ex) Gram staining, Acid fast stain, endospore stain and capsule staining.

Question 40

Do you know the purpose of Gram staining, acid-fast staining and endospore staining? What types of microbes/diseases are they used for?

Answer 40

Gram staining: differential staining procedure that involves multiple steps, an effective method to distinguish between bacteria with different types of cell walls. a few examples of bacteria used are Staphylococcus aureus and Escherichia coli (E.coli).

acid-fast staining: is able to differentiate two types of gram-positive cells: those that have waxy mycolic acids in their cell walls, and those that do not. examples Mycobacterium tuberculosis

endospore staining: uses two stains to differentiate endospores from the rest of the cell. example of microbes is Bacillus subtilis.

Question 41

Do you know the purpose of Gram staining, acid-fast staining and endospore staining? What types of microbes/diseases are they used for?

Answer 41

Gram staining: differential staining procedure that involves multiple steps, an effective method to distinguish between bacteria with different types of cell walls. a few examples of bacteria used are Staphylococcus aureus and Escherichia coli (E.coli).

acid-fast staining: is able to differentiate two types of gram-positive cells: those that have waxy mycolic acids in their cell walls, and those that do not. examples Mycobacterium tuberculosis

endospore staining: uses two stains to differentiate endospores from the rest of the cell. example of microbes is Bacillus subtilis.

Question 42

What is organic chemistry? Why is carbon so important for life? Do you know the difference between structural isomers and optical isomers (enantiomers)?

Answer 42

Organic chemistry is the discipline devoted to the study of carbon-based chemistry, which is the foundation for the study of biomolecules and the discipline of biochemistry.
Carbon is very important because it can form stable bonds with many elements including itself.
Isomers are molecules with the same atomic makeup but different structural arrangement of atoms.
Enantiomers are molecules that have the characteristic of chirality, in which their structures are nonsuperimposable mirror images of each other.

Question 43

Describe a few functional groups and why they are important in biological molecules.

Answer 43

hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl groups
hese groups play an important role in the formation of molecules like DNA, proteins, carbohydrates, and lipids.

Question 44

What are the four classes of macromolecules important in our body? Do you know the names of the monomers and the polymers in each case?

Answer 44

Carbohydrates: glucose, galactose, fructose

Protein: amino acids

Lipids: triglycerides

Nucleic Acid: nucleotides

Question 45

What are dehydration and hydrolysis reactions? Do you know the purpose and example of each?

Answer 45

A dehydration reaction is the formation of a polymer by removing water and linking together two monomers. It is important for dehydration synthesis to serve as a chemical basis for the building of larger macromolecules. An example is two glucose molecules forming together to form maltose.

A hydrolysis reaction is opposite to a dehydration reaction, where the addition of water breaks down large molecules into their subunits. This synthesis plays an important role to your body by breaking down food into nutritious components. An example can be one maltose molecule splitting into two glucose molecules.

Question 46

What is the main function of carbohydrates? Do you know who (plants, animals or bacteria) produces glycogen, cellulose and starch? What monosaccharides are needed to build these polysaccharides?

Answer 46

The main function of carbohydrates is long-term and short-term energy source.

• Plants synthesize cellulose for cell wall components.
• Animals and bacteria produce glycogen as their primary source of energy.
• Starch is synthesized by plants and is their primary source of energy.

Glycogen, cellulose and starch all need the monosaccharide glucose to be built.

Question 47

Lipids are made of hydrocarbons, and they tend to be hydrophobic. Can you recognize the structures and functions of triglycerides, phospholipid and cholesterol? What’s the difference between saturated and unsaturated fats?

Answer 47

Triglyceride is composed of one molecule of glycerol and
three molecules of fatty acids

Saturated fat has single bonds and is solid at room
temperature

Unsaturated fat contains double bonds and is liquid at room
Temperature

Phospholipids are the
primary components of
cellular membranes

A phospholipid contains one molecules of glycerol, 2 fatty
acids and a polar phosphate group

It contains a polar head (hydrophilic) and two nonpolar tails

hydrophobic)
This is called amphipathic

2 layers of phospholipids form lipid bilayer, the structure of cell membrane

Steroids are lipids that have a backbone of four fused rings

Cholesterol is an important biological molecule that plays a
key role in cell membrane structure

Estrogen and testosterone are sex hormones

Cholesterol is the basis of estrogen and
testosterone

When exposed to water, a single layer of phospholipids forms a micelle

Question 48

Give two examples of functional significance of steroids in humans.

Answer 48

Cortisol, our main stress hormone, allows our bodies to respond to threatening situations (or situations which we perceive as threatening). It augments our catabolism of glucose and our ability to heal our own tissue, amongst various other functions.
Aldosterone is another steroid hormone in our bodies with the vital function of maintaining homeostasis via regulation of salts and water in our bloodstreams and tissues.

Question 49

Draw the basic structure of an amino acid, and show where the ‘R’ group is. How many amino acids are there in the human body, and how are they different from each other?

Answer 49

THe unique characteristics of the group allows these components to form hydrogen, ionic, and disufide bonds, along with polar/nonpolar interactions needed to form secondary, tertiary, and quaternary proteins structures
Approximately 50 for polypeptides, 20 for oligopeptides
Th number of monomers along with variety of possible R groups on each amino acid allows for a nearly unlimited diverse types of proteins

Question 50

What important functions do proteins have in a cell? Give some examples. How many levels of organization are there for protein structures?

Answer 50

The major functions of proteins are providing structure, regulating body processes, transporting materials, balancing fluids, helping with immunity, and providing energy. this includes anti bodies, they are also a last resort source of energy once the body has ran out of carbohydrates and fats.
There are 4 levels of protein structure organization, primary is first which is a chain of peptides, secondary is the local folding of the polypeptide chain into a sheet, tertiary structure is three dimensional because of side chain interactions, quaternary structure is a protein consisting of more than one amino acid chain.

Question 51

Heating a protein sufficiently may cause it to denature. Considering the definition of denaturation, what does this statement say about the strengths of peptide bonds in comparison to hydrogen bonds?

Answer 51

Hydrogen bonds are weak, peptide bonds are strong

Question 52

What are the organs and defenses of URT and LRT? Do they have normal biota?

Answer 52

URT - Upper Respiratory Tract

Organs: Pharynx, Nasal Cavity
Defenses:

Mucosa-associated lymphoid tissue (MALT), including adenoids and tonsils
Secreted antibodies (IgA)
Lysozyme
Surfacant
Antimicrobial peptides (AMPs) called defensins
Do they have normal biota?

URT contains an abundant and diverse microbiota.

LRT - Lower Respiratory Tract

Organs:

Bronchi
Bronchioles
Trachea
Aveoli

Defenses:

Alveolar macrophages
Mucociliary Escalator
Do they have normal biota?

It is unclear at this time if these small populations of bacteria constitute a normal microbiota or if they are transients.

Question 53

What are some respiratory defenses? What is the mucociliary escalator? Do you know the function of goblet cells?

Answer 53

Some respiratory defenses are the mucociliary escalator, the cough reflex, and alveolar macrophages(catches particles <2 µm that reach the respiratory units beyond bronchioles, rich in defense elements).
The mucociliary escalator is made up of cilia and mucus. It moves mucus up and out of the lungs where it can be expelled by swallowing or coughing.
Goblet cells are epithelial(line the internal and external surfaces of the body) cells that line and maintain many mucosal surfaces. They also secrete antimicrobial proteins, chemokines, and cytokines.

Question 54

What are the signs and symptoms of COVID-19? How does the disease progress in severe patients? What is a cytokinefive i storm? What is ARDS?

Answer 54

The signs and Symptoms of COVID-19 are mild cough, fatigue, fever/chills, muscle aches, headaches, difficulty breathing/shortness of breath, loss taste or smell, nausea/vomiting, diarrhea, runny nose, and/or sore throat. These symptoms could appear 2-14 days after contact exposure to a someone that has COVID-19. Patients that are affected severely from this virus could experience persistent paint/pressure on their chest, inability to wake or stay awake, trouble breathing, and/or having pale, gray, or blue-colored skin/lips/nails. Cytokine storm is known to damage the lung cells. By having the macrophages identify the virus, hence produces more cytokines. The more cytokines are produced the more it attracts the white blood cells, which could produce more cytokines, thus creating a cycle of inflammation and damage towards the lung cells. Acute Respiratory Distress Syndrome (ARDS) is where the air sacs becomes filled with fluid that leaks from tiny blood vessels within the lungs. Then shortness of breath begins to take place, hence lung failure. Often times patients with ARDS would have really hard time breathing to the point where they must required ventilator to assist with their breathing.

Question 55

What is the causative agent COVID-19, and what kind of genome does it have? Why do scientists think the virus probably jumped to a human host from a bat or a pangolin?

Answer 55

The Coronaviruses are a group of enveloped viruses that are highly pathogenic. The causative agent for COVID-19 is caused by SARS-CoV-2, a more pathogenic form than previously identified SARS-CoV (2002) and Middle East respiratory syndrome coronavirus (MERS-CoV, 2013).

CoVs belong to the Coronaviridae family of order Nidovirales. They have been classified into four genera that include α-, β-, γ-, and δ-coronaviruses. Among them, α- and β- CoVs infect mammals, γ-coronaviruses infect avian species, and δ-coronaviruses infect both mammals and aves. It has a positive single-stranded RNA genome. The discovery of RaTG13 bat coronavirus in China suggested a high probability of a bat origin. Zhou et al. identified a closely related SARSr-CoV genome sequence, RaTG13, which shared a 96% whole-genome sequence identity with SARS-CoV-2, Whole genome sequences were obtained from five independent bats (Rhinolophus acuminatus) in a Thai cave yielding a single isolate (named RacCS203) which is most related to the RmYN02 isolate found in Rhinolophus malayanus. SARS-CoV-2 neutralizing antibodies were also detected in bats of the same colony and in a pangolin at a wildlife checkpoint in Southern Thailand. If bats can be found with antibodies fighting similar coronavirus strains, they believe the jump from origin host to human is not entirely surprising.

Question 56

What receptor does SARS-CoV-2 bind to on host cells? Do you know its life cycle? Are all coronaviruses pathogenic?

Answer 56

SARS-CoV-2 binds to the human ACE2 (hACE2) receptor on host cells.

The life cycle of COVID starts like this. The first 5 days is the incubation period, where the virus starts to enter a healthy cell and start reproducing / duplicating itself. This happens inside the cell so the immune system won’t respond. From 5-14 days after, the amount of virus in your system has started to hit levels where your immune system is alerted and releases cytokines to fight the infection. Usually by 14 days, a healthy host will not be infected. For those who are older in age or are immunocompromised, more severe symptoms may occur from day 14 - 21. Signs may include shortness of breath to pneumonia. If the patient is still showing symptoms, from day 21-60 is the time frame that there may be a chance that death might occur.

Not all coronaviruses are pathogenic. Some like MERS-COV and SARS-COV can cause illness in humans and animals while other coronaviruses are harmless.

Question 57

What are SARS-CoV-2 variants? What kinds of mutation can make a variant more transmissible?

Answer 57

A: There are many variants of the SARS-CoV-2 virus, because the process of viral replication relies on RNA polymerase. RNA polymerase lacks the ability to “proofread” the replicated genome the same way that DNA polymerase can (Virology blog) which results in a higher rate of mutations. Any virus carrying a mutation is recognized as a variant. Depending on where the mutation occurs in the sequence of the virus, the properties can be changed. This includes the transmissibility. Changes to the spike proteins typically can increase transmissibility. For example a change to the amino acid sequence in the spike protein could allow the virus to bind more tightly to the ACE2 receptor, or reduce the binding between the spike protein and antibodies in our body generated by immune response or vaccination.

The Delta variant was the dominant variant of summer 2021 and had high transmissibility rates. Researchers found that a specific mutation in the delta variant known as P681R mutation, allowed the delta variant to outperform all others and become the dominant variant. The P681R mutation specifically changes the amino acid sequence (proline into an arginine) in a very specific section of the spike protein known as the furin cleavage site.

Question 58

How is SARS-CoV-2 transmitted? What is the basic reproductive number? What is herd immunity?

Answer 58

SARS-CoV-2 is transmitted by exposure to infectious respiratory fluids.
it has been estimated that SARS-CoV-2 has a R0 = 2-2.5
Herd immunity occurs when a large portion of a community (the herd) becomes immune to a disease. The spread of disease from person to person becomes unlikely when herd immunity is achieved. As a result, the whole community becomes protected — not just those who are immune.

Question 59

How is COVID-19 diagnosed? Do you know the differences between the different testing methods?

Answer 59

To test for Covid 19, a swab sample is taken from the nose (nasopharyngeal), throat, or saliva. The sample is sent to the laboratory for testing. There are different type of test to detect the virus. The viral test also known as the nucleic acid amplification tests (NAATs) is a PCR based test that detects the viral genetic material. The antigen test is a rapid test and some can be done at home. The last method is the antibody test which looks for antibodies in the blood.

Question 60

What is the best prevention of COVID-19? Do you know the differences between the vaccines? What are some behaviors to prevent from getting infected?

Answer 60

Different types of vaccines work in different ways to offer protection. But with all types of vaccines, the body is left with a supply of “memory” T-lymphocytes as well as B-lymphocytes that will remember how to fight that virus in the future

mRNA vaccines contain material from the virus that gives our cells instructions for how to make a harmless protein (spike protein) that is unique to the SARS-CoV-2. After our cells make copies of the protein, they destroy the genetic material from the vaccine. Our bodies recognize that the protein should not be there and build T-lymphocytes and B-lymphocytes that will remember how to fight the virus if we are infected in the future.

Protein subunit vaccines include harmless pieces (proteins) of the virus instead of the entire germ. Once vaccinated, our bodies recognize that the protein should not be there and build T-lymphocytes and antibodies that will remember how to fight SARS-CoV-2 if we are infected in the future.

Vector vaccines contain a modified version of a different virus such as adenovirus as a “vector” to deliver genetic material (spike protein gene) to our cells. Once the viral vector is inside our cells, the genetic material gives cells instructions to make the spike protein. This prompts our bodies to build T-lymphocytes and B-lymphocytes that will remember how to fight the virus if we are infected in the future.

Question 61

What are some treatments for COVID-19 patients at different stages of the disease?

Answer 61

In the early stages of infection, antivirals and interferons are good pharmaceutical options to treat COVID-19, because they interfere with the virus’ ability so infect more host cells. This of course lowers the risk that the infection will progress to more serious stages and spread further throughout the body. Another treatment in early stages can be the use of neutralizing antibodies, either from recovered COVID-19 patients or man-made monoclonal antibodies, which mimic the role of human antibodies in the body. These antibodies bind to the spike protein on the virus. Because the spike protein is like a key the virus uses to attach to the ACE-2 receptor and enter the cell, antibodies can prevent infection by attaching to the spike protein and blocking entry. These antibodies also act as a flag to the immune system to kill the virus or infected cells they’re attached to.

During later, more serious stages of infection, the body’s own immune response is the main cause of severe symptoms. This is often the result of a “cytokine storm” caused by over production of cytokines leading to inflammation and damage to lung cells. Sometimes this damage is irreversible. That’s why reducing inflammation is the most important treatment at later stages. Medical professionals can administer anti-inflammatories such as corticosteroids to “calm” the immune system, reducing inflammation and limiting damage to lung cells. This not only improves recovery time, but can also potentially reduce the long term effects some patients experience due to damage to their lung cells.

Question 62

Who was the father of modern genetics and what was his contributions? Do you know the significance of the ‘chromosomal theory of inheritance’?

Answer 62

The man dubbed the father of modern genetics is named Gregor Mendel. One of his greatest contributions is the discovery the fundamental laws of inheritance. In simple words, the law of inheritance states that each “parent” gives one allele that combines in the fertilization process.

The chromosomal theory states “chromosomes are the vehicles of genetic heredity”. In simple words, the theory explains that genes are units of inheritance that are responsible for our features and traits. There are multiple factors that enlightens us on how genetics works. One factor would be how dominate traits override the recessive traits. Another factor would be how genetic information is passed down. During cell division when egg and sperm meet, called meiosis, chromosomes are moved around and mixed, leading to offspring that is genetically diverse. Lastly, the fact that mutations can happen in chromosomes. This gives us insight on the diseases we may have because of misprinted genetic information.

Question 63

How did Griffith define ‘transforming principle’? Whose work led to the discovery of the identity of ‘transforming principle’?

Answer 63

Answer: Griffith had discovered that he could convert the R strain into the virulent S strain. After he injected mice with R strain cells and, simultaneously, with heat-killed cells of the S strain, the mice developed pneumonia and died. In their blood, Griffith found live bacteria of the deadly S type.

The principle was able to transform a non-pathogenic bacteria into a pathogenic strain

Question 64

Can you describe the experiment performed by Hershey and Chase, and explain why it was conclusive in convincing the scientific community that DNA was the genetic material?

Answer 64

Alfred Hershey and Martha Chase performed their own experiments in 1952 and were able to provide confirmatory evidence that DNA, not protein, was the genetic material (Figure 10.9). Hershey and Chase were studying a bacteriophage, a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The particular bacteriophage they were studying was the T2 bacteriophage, which infects E. coli cells. As we now know today, T2 attaches to the surface of the bacterial cell and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages.
Hershey and Chase labeled the protein coat in one batch of phage using radioactive sulfur, 35S, because sulfur is found in the amino acids methionine and cysteine but not in nucleic acids. They labeled the DNA in another batch using radioactive phosphorus, 32P, because phosphorus is found in DNA and RNA but not typically in protein.

Each batch of phage was allowed to infect the cells separately. After infection, Hershey and Chase put each phage bacterial suspension in a blender, which detached the phage coats from the host cell, and spun down the resulting suspension in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube with the protein labeled, the radioactivity remained only in the supernatant. In the tube with the DNA labeled, the radioactivity was detected only in the bacterial cells. Hershey and Chase concluded that it was the phage DNA that was injected into the cell that carried the information to produce more phage particles, thus proving that DNA, not proteins, was the source of the genetic material. As a result of their work, the scientific community more broadly accepted DNA as the molecule responsible for heredity.

Only the DNA of a bacteriophage (virus that infects bacteria) is needed to infect/hijack it

Question 65

What are DNA and RNA made of? How many nucleotides are there for DNA vs. for RNA? How are they different from each other?

Answer 65

A nucleotide is the basic building block of nucleic acids (RNA and DNA). A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base. The bases used in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T).

There are two differences that distinguish DNA from RNA: (a) RNA contains the sugar ribose, while DNA contains the slightly different sugar deoxyribose (a type of ribose that lacks one oxygen atom), and (b) RNA has the nucleobase uracil while DNA contains thymine.

Question 66

What is the backbone of DNA/RNA made of? Look at a strand of DNA or RNA and see if you can figure out why one end is called the ‘5 prime’ end and the other is called the ‘3 prime’ end (represented by 5’ and 3’). Use an image to explain.

Answer 66

The sugar-phosphate backbone forms the structural framework of nucleic acids, including DNA and RNA. This backbone is composed of alternating sugar and phosphate groups, and defines directionality of the molecule.

Question 67

What are some features of DNA structure? Who are the scientists who discovered this double helix structure?

Answer 67

Each molecule of DNA is a double helix formed from two complementary strands of nucleotides held together by hydrogen bonds between G-C and A-T base pairs. Each strand has a backbone made of alternating sugar (deoxyribose) and phosphate groups. Attached to each sugar is one of four nitrogen bases: adenine (A), cytosine (C), guanine (G) or thymine (T). Duplication of the genetic information occurs by the use of one DNA strand as a template for formation of a complementary strand.

In the early 1950s, American biologist James Watson and British physicist Francis Crick and British biophysicist Maurice Wilkins developed their model of the DNA double helix structure with the help of British Chemist Rosalind Franklin’s technique X-Ray crystallography. Franklin and her student produced images of DNA using X-ray crystallography. The famous “image 5” a remarkably clear and striking X-ray diffraction image of DNA.

for RNA Uracil replaces Thymine, binds to Adenine

Question 68

What bonds stabilize the DNA double helix? What is DNA denaturation?

Answer 68

Hydrogen bonds stabilize the DNA double helix.
Base Pairs A-T and C-G
Adenine and Thymine Pair forms 2 H bonds
Cytosine and Guanine forms 3 H bonds
DNA denaturation- When (H) bonds are broken. Separating the double helix of DNA into a single strand

Question 69

What’s the main function of DNA vs. RNA? How does the structure of RNA differ from that of DNA?

Answer 69

The main function of DNA (deoxyribonucleic acid) is to store the information needed to build and control the cell. The transmission of this information from mother to daughter cells is called vertical gene transfer and it usually occurs through the process of DNA replication. DNA is replicated when a cell makes a duplicate copy of its DNA, then the cell divides, resulting in the correct distribution of one DNA copy to each resulting cell. DNA however does not serve a structural role in cells. RNA (ribonucleic acid) molecules perform a variety of roles in the cell but are mainly involved in the process of protein synthesis (translation) and its regulation. RNA has three main types that are directly involved in protein synthesis which are messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA).

DNA and RNA are quite similar to each other. The difference is that DNA molecules are typically long and double stranded and RNA molecules are much shorter and are typically single stranded. An image I saw from Openstax shows the structure difference of a DNA and RNA.

Question 70

Can you describe the structure and function of mRNA, rRNA and tRNA? How do they serve a role in protein synthesis?

Answer 70

mRNA stands for messenger RNA and is the strip of genetic material copied from the DNA in the nucleus that is sent out into the cytoplasm for translation into a protein. rRNA stands for ribosomal RNA which makes up the ribosomes that help conduct protein synthesis. This mechanism joins with tRNA (transfer RNA), which string together amino acids coded for by the mRNA to build proteins.

Question 71

Can you distinguish genotype vs. phenotype? What is the definition of genome?

Answer 71

The genotype is an organism’s genetic information, while the phenotype is the observable physical traits or attributes.

Genotype is the unique sequence of DNA. Is it distinguishable as it is unique to the cell. The two alleles present create the DNA for this organism, it is all part of the genetic makeup.

Phenotype refers to the patient’s clinical presentation or findings. What is observable.

Genome is defined as the complete set of genes or genetic material present in a cell or organism.

Question 72

How are eukaryotic chromosomes packaged differently than prokaryotic chromosomes? What kind of extrachromosomal DNA would you find in each type of cell?

Answer 72

Eukaryotic cells have a nucleus and chromosomes are located in the nucleus. While for Prokaryotic cells that lack a nucleus, chromosomes are found in the nucleiod. Eukaryotes cells wrap DNA around a protein called histones to help contain the DNA in a smaller space.Most prokaryotic cells do not contain histones so the compress DNA through supercoiling .

Question 73

What is ‘Spontaneous generation’? Whose experiment definitively disputed this idea? Describe the experiment.

Answer 73

Greek philosopher Aristotle was one of the earliest scholars to articulate the theory of spontaneous generation, the notion that life can arise from nonliving matter. Aristotle attributed the ability for nonliving material to give life, if that nonliving material contained pneuma (“spirit” or “breath”).

Italian physician Francesco Redi, performed an experiment that refuted the idea that maggots spontaneously generate on meat left out in the open air. He used 6 containers, 2 were left open giving direct access to the meat, 2 were sealed preventing access, and 2 were covered by gauze. Maggots were found on the meat with the open containers, and on top of containers with gauze but not on the meat itself, but were not present on the sealed container. He concluded that maggots could only form when flies were allowed to lay eggs in the meat, and that the maggots were the offspring of flies, not the product of spontaneous generation.

Louis Pasteur ended the debate over spontaneous generation when he used a series of flasks with long, twisted necks. He would boil the broth inside the flask until it became sterilized, and predicted that as long as the swan neck prevented airborne microorganisms, that the flasks would remain sterile, and if the neck was broken that airborne microbes would be responsible for microbial growth within the flask.

Pasteur articulated “Omne vivum ex vivo” (“Life only comes from life”).

Question 74

What are the three parts of ‘Cell theory’? How and when did eukaryotes evolve? What is the ‘Endosymbiotic theory’, and do you know the supporting evidence for it?

Answer 74

All living things are composed of cells.
Cells are the basic units of structure and function for living things.
All cells come from pre-existing cells. Also, organisms grow by “adding on more cells” NOT by increasing the size of their cells.

2.7 billion years ago

The hypothesis that eukaryotic cells evolved from a symbiotic association of prokaryotes—endosymbiosis—is particularly well supported by studies of mitochondria and chloroplasts, which are thought to have evolved from bacteria living in large cells.

The endosymbiotic theory posits that some eukaryotic cell organelles, such as mitochondria and plastids, evolved from free-living prokaryotes. Available data indicate that the mitochondrial endosymbiosis initiated the evolution of the eukaryotic cell, as suggested by Margulis.

Question 75

What is the “Germ Theory of Disease”? Explain how the work done by Lister and Semmelweis supports the germ theory of disease.

Answer 75

In the 1500’s, Girolamo Fracastori was the first person to say that disease might be spread by “seed-like entities”; he categorized them by way of transmission. Agonisto Bassi theorized that disease in humans and animals was caused by microorganisms; he studied silkworms with disease caused by parasites. Louis Pasteur is accredited with the “germ theory of disease”, which is defined as such:

Many disease are caused by infections with many species of microorganisms, such as bacterial, viral, fungal, or protists.

Joseph Lister was the first to apply the “germ theory of disease” to surgery. He developed antiseptic techniques through experimentation and clinical trials. The evidence that Lister’s antiseptic techniques spoke for itself, and his techniques were widely accepted by surgeons around the world.

Ignaz Semmelweis was a Hungarian doctor that studied childbed fever in two maternity wards. He discovered that women in one clinic where doctors were performing births were dying 5x faster than in another clinic with only midwives. This was because the doctors were performing autopsies, washing their hands and instruments with only soap, and then delivering babies. When Semmelweis ordered medical staff to clean with a chlorine solution as well as more vigorous hand-washing, the rate of disease in these women fell dramatically.

Both Lister and Semmelweis showed that trying to kill as many disease-causing microorganisms by keeping standards of cleanliness prevents infection with their work, supporting the germ theory of disease.

Question 76

How did John Snow, Louis Pasteur and Robert Koch each contributed to the germ theory? Do you know the different steps of the ‘Koch postulates’?

Answer 76

John Snow was able to prove that cholera bacteria were being transmitted by contaminated drinking water. He was able to do this by plotting all of the affected people’s locations on a map and saw most of the plots were in one neighborhood, which led him to find a contaminated water supply in that neighborhood. This proved that the bacteria transmission was not from the air or smell like others though at the time. Louis Pasteur did an experiment with a swan-neck flask that disproved spontaneous generation. The curve of the flask prevented outside air from entering the flask so no bacteria grew in the broth. When the neck of the flask was broken off bacteria was able to grow in the broth. Pasteur also discovered fermentation and proved that food spoiled because of bacteria contamination, not from spontaneous generation. Robert Koch found that a particular germ could cause a specific disease. He discovered this while studying anthrax. This led to the discovery of the causative agents for many bacterial infections. The first step in Koch’s postulates is collecting microorganisms from an organism with the disease, not healthy individuals. Then the microorganism is isolated and grown in a pure culture. The cultured microorganism is then introduced into a healthy organism and the disease is reproduced. The pathogenic microorganism is then isolated and grown in a pure culture and should be identified as being identical to the original causative agent.

Question 77

What is the structure and main function of plasma membranes? List 3 mechanisms for molecules to cross the plasma membrane. Give an example of each and briefly explain.

Answer 77

It has two hydrophilic sides with the middle hydrophobic layer. This “sandwich” structure allows the phospholipids to form a micelle structure that allows separation between the inner cell environment and outer cell environment, so inside and outside the cell can be different. Since the middle layer of the membrane is hydrophobic, small and nonpolar molecules, such as carbon dioxide, can pass through the membrane. Water may use facilitated diffusion such as going through aquaporin to get in the cell faster. Potassium and Sodium are charged, so they cannot cross the membrane easily. They need to use sodium/potassium pump, which is a form of active transport, to cross the membrane.

Question 78

How are bacterial chromosomes different from eukaryotic chromosomes? What is the area in a bacterial cell where the chromosome is located called? What is a plasmid?

Answer 78

The DNA molecules of bacterial chromosomes have a slightly different structure than those of eukaryotic chromosomes. Eukaryotes have a single circular chromosome, whereas bacteria have several linear chromosomes. Bacterial chromosomes have much more protein associated with the DNA than eukaryotes.
Bacterial chromosomes are located in a nucleoid, a distinct cytoplasmic structure, in which double-stranded DNA is coated with histone-like proteins. Most bacteria appear to have a single large circular chromosome, but this is not universal.

a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. That doesn’t carry essential genes

Question 79

What is a bacterial “capsule”? Why do we care about bacteria with capsules in a clinical setting? What is biofilm, and where would you find it?

Answer 79

A bacterial capsule is formed by many pathogenic bacteria that serves as protection against phagocytosis (when living cells ingest other cells). Its capsular coating blocks the mechanisms that phagocytes use to attach and engulf bacteria. This is important to us because it enhances the ability of bacteria to cause disease.

Biofilm is film that are formed by free-living bacteria that protect a mature community of additional microbes with complex functions. Wherever you find a combination of moisture, nutrients, and a surface, you are likely to find biofilm.

Question 80

What is the difference between fimbriae and flagella? What are the functions of each?

Answer 80

Fimbriae are bristle like fibers filamentous, common with bacteria. It can be used for motility and also attachment to host cells. Fimbriae can also help with the formation of biofilms.
Flagella are long whip shaped filamentous, common with bacteria. Flagella, used mostly for motility, but can be used to sense temperature and certain chemicals of interest in the environment. they can be present in prokaryotes and eukaryotes

Function of flagella is locomotion. Flagella are appendages that go through the cell membrane. They are long and whip shaped.
Function of fimbriae is surface attachment. Fimbriae are hollow extensions that go through the cells surfaces. They are shorter and involved in bacterial conjugation.

Question 81

Draw the different layers of the skin and label the defense mechanisms of the skin on your drawing.

Answer 81

Multiple layers of skin cells in the epidermis act as physical barrier
Stratum corneum contains dead cells that shed constantly taking bacteria attached with them

Antimicrobial peptides (AMPs) and lipids act as chemical barriers
Acidic pH of the skin acts as a chemical barrier
Immune cells of the skin

Normal microbiota of the skin

Multiple layers of skin cells in the epidermis act as physical barrier
Stratum corneum contains dead cells that shed constantly taking bacteria attached with them
Antimicrobial peptides (AMPs) and lipids act as chemical barriers
Acidic pH of the skin acts as a chemical barrier
Immune cells of the skin
Normal microbiota of the skin

Question 82

What is the oxygen requirement of Pseudomonas aeruginosa? Does it explain why it often causes infection in cystic fibrosis patients’ lungs?

Answer 82

Pseudomonas aeruginosa is an obligate aerobe, meaning it needs oxygen to survive. This explains why it often causes infection in the lungs of CF patients as there is an abundance of oxygen in the lungs.
I did some more research on Psuedomonas infections in the lungs of those with cystic fibrosis and found it interesting that the bacteria is opportunistic meaning that they solely cause infection in those who are immunosuppressed or who have a condition such as cystic fibrosis.

Question 83

How does the size of the P. aeruginosa genome compare with that of E. coli and S. aureus? What’s the implication of the large genome size and large number of genes?

Answer 83

P. aeruginosa has a larger genome than those of the two other major nosocomial pathogens Escherichia coli and Staphylococcus aureus that have an average size of 4,721 and 3,118 genes, respectively [33, 34]. The ubiquity of P. aeruginosa relies on its metabolic versatility and on the large range of its hosts.

Question 84

What are some virulence factors of P. aeruginosa? What helps them form biofilms? Why are biofilms harder to treat?

Answer 84

The extrapolymeric substance (EPS), or glycocalyx, allows the bacteria to adhere to the host cells and makes it harder for the host to physically remove the pathogen

The EPS not only allows for attachment but provides protection against the immune system and antibiotic treatments, preventing antibiotics from reaching the bacterial cells within the biofilm. In addition, not all bacteria in a biofilm are rapidly growing; some are in stationary phase. Since antibiotics are most effective against rapidly growing bacteria, portions of bacteria in a biofilm are protected against antibiotics.

Question 85

How is P. aeruginosa infection diagnosed? How are skin infections transmitted and prevented?

Answer 85

P. aeruginosa can be detected through the use of cetrimide agar, which is selective for Pseudomonas species (Figure 21.17). Samples of blood or other body fluids are sent to the clinical labs for bacterial cultures. The production of blue-green pigments in colonies on agar plates (Figure 21.17b) is an indication of P. aeruginosa. Drug susceptibility tests are usually included because P. aeruginosa is known to be resistant to multiple antibiotics.
keep their hands clean to avoid getting sick and spreading germs that can cause infections
wash their hands with soap and water or use alcohol-based hand sanitizer, particularly before and after caring for wounds or touching a medical device
remind healthcare providers and caregivers to clean their hands before touching the patient or handling medical devices
allow healthcare staff to clean their room daily when in a healthcare setting

Question 86

Are P. aeruginosa infections easy or hard to treat and why? How is antibiotic resistance tested? What is the zone of inhibition?

Answer 86

P. aeruginosa are resistant to pretty much all common antibiotics(antimicrobial agents), making it hard to treat it. This is due because of the low permeability of its outer membrane. There’s a test called ExAST which test cultures the germ and sees how sensitive it can be to different antibiotics. Also, the Zone of Inhibition is another test used to see the areas where the bacteria grows around the antibiotic that is being examined.

Question 87

How are proteins made? Where do transcription and translation happen in the eukaryotic cell? How about in a prokaryotic cell?

Answer 87

In order for a cell to manufacture these proteins, specific genes within its DNA must first be transcribed into molecules of mRNA; then, these transcripts must be translated into chains of amino acids, which later fold into fully functional proteins.

in eukaryotes, while transcription occurs in the nucleus, translation occurs in the cytoplasm.

For this reason, most of the cellular processes in the bacteria, including transcription and translation takes place in the cytoplasm of the prokaryotic cell. In fact, both transcription and translation in bacteria are coupled, i.e, both occur simultaneously. This is unlike that of eukaryotic cells, wherein transcription occurs in the nucleus and the mRNA is then taken to the cytoplasm for translation.

Question 88

What is the main function of the nucleus? What is nucleolus and what is its function? What would be its equivalent in a mini city?

Answer 88

The primary functions of the nucleus are to store the cell’s DNA, maintain its integrity, and facilitate its transcription and replication.

The nucleolus is a prominent nuclear condensate that plays a central role in ribosome biogenesis by facilitating the transcription and processing of nascent ribosomal RNA (rRNA).

Townhall

Question 89

In eukaryotic cells, where would you find 80S chromosomes, and where would you find 70S chromosomes? Where are cytoplasmic proteins synthesized? How about secretory and membrane proteins?

Answer 89

The cytoplasmic chromosome of eucaryotes are 80 S. They occur inside the cytoplasm of eukaryotes either freely or attached to ER.

They contain 70s ribosomes in mitochondria and chloroplasts. Eukaryotic cells have evolved an endomembrane system, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.

Protein synthesis occurs in the cytoplasm on ribonucleoprotein particles, the ribosomes.

rough endoplasmic reticulum (rough ER)

Question 90

Which organelles are part of the endomembrane system? What are their functions? What would be their equivalents in a mini city? What service do they provide for the city, and what happens to the city if they do not function properly?

Answer 90

Endomembrane System

Endoplasmic Reticulum: An array of tubules and cisternae (flattened sacs) connected with a single lipid bilayer. The spaces inside the cisternae are called the lumen. In a city, the ER would be a parts factory. Without the ER, the cell wouldn’t have the proteins and lipids it needs for all of it’s organelles.

   Rough ER: Bound on the cytoplasmic side of the membrane are ribosomes             that make proteins that will be inserted into the membrane of the RER. Small         sacs of these proteins will then bud off as transport vesicles from the RER                 membrane and travel to either the golgi apparatus, the plasma membrane,             the membrane of another organelle, or out of the cell.

   Smooth ER: Does not have ribosomes, involved in the biosynthesis of lipids,           carbohydrate metabolism, detoxification of toxic compounds within the cell

Golgi apparatus: composed of membranous disks called dictyosomes, each having a single lipid bilayer, that are stacked together. Enzymes in the golgi apparatus modify lipids and proteins from the ER via transport vesicles, often adding carb components to them, producing glycolipids, glycoproteins, or proteoglycans. These new modified proteins and lipids leave the golgi apparatus via transport proteins and either fuse with the plasma membrane or the membrane of another organelle. In a city, golgi apparatus would be both a factory and packing plant. Without the golgi, the proteins and cells would be simpler and our cells wouldn’t be as specialized and variable in terms of function. I.e. glycolipids and glycoproteins modified in the GA are often inserted into the plasma membrane and are important for signal recognition by other cells or infectious particles

Lysosome: membrane bound organelles that contain digestive enzymes, usually used to break down food, damaged organelles, cellular debris, microorganisms, immune complexes. In a city, lysosomes would be recology. Without lysosomes, the cell couldn’t break down potentially harmful and unnecessary particles.

Question 91

Do you know the structure and function of mitochondria? What would be its equivalent in a mini city? What service does it provide for the city, and what happens to the city if it does not function properly?

Answer 91

Mitochondria are membrane-bound cell organelles (mitochondrion, singular) that generate most of the chemical energy needed to power the cell’s biochemical reactions. Chemical energy produced by the mitochondria is stored in a small molecule called adenosine triphosphate (ATP).

Power plant

If it stops everything in the cells dies from lack of ATP to power

Question 92

What are cytoskeleton molecules? What function do they have in cells?

Answer 92

There are three cytoskeleton molecules, the microfilaments, or actin filaments, the intermediate filaments, and the microtubules.

Microfilaments allows for mobility within the cell, typically with cell division and vesicle transportation. It also helps with the rigidity of the cell. It’s ability to depolymerize and repolymerize provides some cells with the ability to change its shape such as macrophages during phagocytosis.

Intermediate filament plays no role in mobility within the cell, its sole purpose is to provide structural support to the cell and anchor organelles.

Microtubules are hollow and they give structure to cilia and flagella. It also plays a key role in mitosis by pulling the two daughter cells away from each other to finalize mitosis.

The microfilaments are the actin filaments. Only eukaryotes have cilia, and both prokaryotes and eukaryotes have flagella, but there are differences in their flagella.

Question 93

What is the extracellular matrix (ECM)? What’s the main function of glycocalyx?

Answer 93

Extracellular matrix (ECM) is the outermost layer of the cell. The ECM is made of proteins and polysaccharides including collagen, proteoglycan and hyaluronic acid. The main functions of glycocalyx are helping the cell adhere to surfaces, aids in the formation of biofilms, helps protect the cell and also acts as a signal sensor. There are two important types of glycocalyx, which are capsules and slime layers.

Question 94

How are bacterial and eukaryotic flagella similar and different from each other? What are cilia made of?

Answer 94

Both used flagella for motility.
Eukaryotic flagella are structurally distinct from prokaryotic cells. Prokaryotic flagella is stiff and rotates. Whereas eukaryotic flagellum is whip like and more flexible, it is composed of 9 paralled pairs of microtubules surrounding a central pair of microtubules, allowing bending, referred to as a 9+2 array arrangement.
Cilia are a external structure found in some eukaryotic cells, cilia are shorter than flagella and often cover the entire surface of a cell, although they use similar motility and are structurally similar to 9+2 array, they are compose of triple microtubules similar to a centriole.

Question 95

Know the normal biota of the different parts of the GI tract, and their functions

Answer 95

These microbes include Bacteriodetes (especially the genera Bacteroides and Prevotella) and Firmicutes (especially members of the genus Clostridium). Methanogenic archaea and some fungi are also present, among many other species of bacteria. These microbes all aid in digestion and contribute to the production of feces, the waste excreted from the digestive tract, and flatus, the gas produced from microbial fermentation of undigested food. They can also produce valuable nutrients.

Peyer’s patches (Figure 24.5), detect pathogens in the intestines via microfold (M) cells, which transfer antigens from the lumen of the intestine to the lymphocytes on Peyer’s patches to induce an immune response. The Peyer’s patches then secrete IgA and other pathogen-specific antibodies into the intestinal lumen to help keep intestinal microbes at safe levels. Goblet cells, which are modified simple columnar epithelial cells, also line the GI tract (Figure 24.6). Goblet cells secrete a gel-forming mucin, which is the major component of mucus. The production of a protective layer of mucus helps reduce the risk of pathogens reaching deeper tissues.

Question 96

For acute diarrhea, know the virulence factors, symptoms, disease transmission and treatment for ETEC and STEC/EHEC.

Answer 96

Decades of research on virulence factor regulation in ETEC has revealed a variety of environmental factors that influence gene expression, including bile, pH, bicarbonate, osmolarity, and glucose. However, other hallmarks of the intestinal tract, such as low oxygen availability, have not been examined.

Shiga toxins (Stxs) are considered the major virulence factors of EHEC involved in the pathogenesis of HUS. It is generally believed that after intestinal infection with EHEC, Stxs cross the intestinal barrier and bind to endothelial cells.

Question 97

What do ETEC and EHEC stand for? What kind of diseases do they cause?

Answer 97

ETEC stands for Enterotoxigenic E. coli which is the causative agent of most traveler’s diarrhea. Symptoms are relatively mild with watery diarrhea. This is usually self-limiting, but if needed, fluoroquinolones, doxycycline, rifaximin, TMP/SMZ is given and antibiotic resistance is sometimes a problem. This is usually diagnosed using a culturing or PCR test.

EHEC stands for Enterohemorrhagic E. coli. EHEC causes intestinal inflammation and diarrhea. This is the most dangerous strains because this strain can cause an epidemic. EHEC can cause disease ranging from relatively mild to life-threatening. Symptoms include bloody diarrhea with severe cramping, but it does not cause any fever. This is self-limiting, but it can lead to hemorrhagic colitis and profuse bleeding which one possible complication is HUS (Hemolytic Uremic Syndrome which causes a serious disease that affects the kidneys and blood clotting system). Antibiotics are usually not recommended due to the risk of HUS

Question 98

For enteric bacteria, what is the O antigen? What is the H antigen? In other words, what does E. coli O157:H7 refer to?

Answer 98

Enteric bacteria are bacteria that commonly live in the intestines of humans and animals with no harm to the host or even be helpful to the host. However, they can still sometimes cause infections under the right conditions. O and H refer to certain antigens that cause pathogenicity in enteric bacteria. O refers to the O side chain of the lipopolysaccharide and H is the flagella. This particular strain of E. coli can cause serious harm to the host in the form of diarrhea and GI illness.

Question 99

How are E. coli infections diagnosed? What are the treatments? How are ETEC and STEC infections treated differently?

Answer 99

The patient stool sample is sent to laboratory to test for the presence of E. coli bacteria. If blood is present in the stool. Bacteria be cultured to identify specific toxins

Such as following:

Shiga toxin-producing E. coli (STEC): This is the bacteria most commonly known for E. coli food contamination. This strain is also called enterohemorrhagic E. coli (EHEC) and verocytotoxin-producing E. coli (VTEC).
Enterotoxigenic E. coli (ETEC): This strain is commonly known as a cause of travelers’ diarrhea.
Enteroaggregative E. coli (EAEC).
Enteroinvasive E. coli (EIEC).
Enteropathogenic E. coli (EPIC).
Diffusely adherent E. coli (DAEC).

The treatment for E. coli - Most infected persons will recover within a few days, without requiring any specific treatment. Maintain hydration and electrolytes. Drinking fluids and consuming electrolytes and rest are the treatment. IV fluids may be required for the most severe cases. The hemolytic uremic syndrome due to Shigella poisoning may require hospitalization, intravenous fluid replacement, blood transfusions, or dialysis. Antibiotics may increase the number of toxins and the risk of hemolytic uremic syndrome, so they are used in only rare cases. They are never used if there’s any suspicion of an enterohemorrhagic E. coli infection. Antidiarrheal medications are also discouraged. They can slow down movement in the colon, also lead to an increase in the concentration of bacterial toxins in the intestines and increase the duration of the infection.

No antibiotic is used when Shiga toxin-producing bacteria are present in STEC.

In ETEC, under rare cases, antibiotics are used for certain traveler’s diarrhea and infant diarrhea only in cases of fever or persistent diarrhea.

Question 100

What are ribosomes made of? How are prokaryotic ribosomes different from eukaryotic ribosomes?

Answer 100

Ribosomes are constructed from protein and ribosomal RNA (rRNA). Eukaryotic ribosomes are larger than prokaryotic ribosomes.

Both types ribosomes are made of two subunits.

Eukaryotes have complete ribosomes that are 80S, prokaryotes have complete ribosomes that are 70S.

(Svedberg “S” as a unit of measure)

The prokaryote ribosome is made of a small subunit 30S and a large subunit 50S.

Eukaryotic ribosomes are comprised of the small subunit 40S, and the large subunit 60S.

(These numbers do not add up to the size of their complete ribosomes, these measures are when they are apart)

Question 101

What are some other names for TB historically? Do you know how many people in the world have been exposed to TB?

Answer 101

Another name for TB was “phthisis” in Ancient Greece, “Tabes” in Ancient Rome, “Schachepheth” in Ancient Hebrew. It was also referred to as “ the white plague” due it would cause paleness in the patients.

According to the World Health Organization, over six million men, 3.4 women, and 1.2 children have been exposed to TB

About a quarter of the global population is estimated to have been infected with TB bacteria,

Question 102

How does TB progress, what are primary, secondary and extrapulmonary TB?

Answer 102

Primary TB - Bacteria enters the lungs, Tubercles are present causing tissue damage

Secondary TB - The tubercles start to liquify and spread to the lungs which can cause severe symptoms such as fever, coughing, weight loss and chest pain

Extrapulmonary TB- Common in young children, the tubercles start to rupture later spreading bacteria to the pulmonary capillaries. Once spread to the capillaries other organs may be compromised

Question 103

Why is Mycobacterium tuberculosis called an acid-fast bacillus/bacteria (AFB)? What component of the cell wall makes it stain positive in acid-fast?

Answer 103

Mycobacteria are called acid-fast bacilli because they are a group of rod-shaped bacteria (bacilli) that can be seen under the microscope following a staining procedure where the bacteria retain the color of the stain after an acid wash (acid-fast).

mycolic acid
The acid-fastness of Mycobacteria is due to the high mycolic acid content of their cell walls, which is responsible for the staining pattern of poor absorption followed by high retention.

Question 104

Do you know some virulence factors that allow M. tuberculosis to survive in macrophages? List 3.

Answer 104

Some mechanisms that M. tuberculosis uses to survive within macrophages include: inhibiting the fusion of phagosomes with lysosomes; inhibiting the release of acid from lysosomes; and protection from reactive oxidation radicals (Figure 4). As a result, the bacteria continue to multiply inside the macrophages.

Question 105

How is TB diagnosed and treated? What are DR-, MDR- and XDR-TB?

Answer 105

There are two main tests that are used to diagnose TB. The first one is TB skin tests or TB blood tests. There are several ways to treat TB depending on the severity of the disease. Treatment can last from 4 to 9 months. Physicians can prescribe antibiotics depending on the regimen picked for the patient and also it depends on the drug susceptibility results. Sometimes the antibiotics will not work which will cause the patient to develop DR TB or drug resistant TB. Furthermore, it also is possible to develop more than one type of DR TB such as MDR(Multidrug resistant) or XDR TB(Extensively drug-resistant). MDR is a more serious subtype where the patient usually is resistant to more than one drug. Then XDR TB is a more serious subtype, but its rare to develop it. Nonetheless, it usually affects patients with very weak immune systems.