exam 2 Flashcards
What are some common symbiotic relationships exhibited by microbes? Give examples.
When two species benefit from each other, the symbiosis is called mutualism
A type of symbiosis in which one population harms another but remains unaffected itself is called amensalism
Commensalism, one organism benefits while the other is unaffected.
If neither of the symbiotic organisms is affected in any way, we call this type of symbiosis neutralism
A type of symbiosis in which one organism benefits while harming the other is called parasitism
What is our microbiota, and what types of relationships do they have with us? Why are they important to our health?
Our microbiota are all the microbes living on our epithelial tissue. Microbes can live on skin, mouth, gut, and vagina. Many of them have mutualistic relationship with us, such as the microbes in our gut to help break down food that our own mechanisms cannot break down. Some of them are commensalism, such as some microbes on the skin that eats dead skin cells, but has no effect to us. Some of the resident microbes are pathogenic, but as long as they are in balance with the beneficial microbes, in other words they are a small proportion compared to the beneficial microbes, then “good” and “bad” microbes can live together. Also, some beneficial microbes can be pathogenic if they grow out of number.
What is the name for when your microbiota is disrupted? How can it affect your health?
Dysbiosis is the term for a disrupted microbiota. It affects fundamental systems in our body, including but not limited to the nervous system, digestive system, respiratory system and the cardiovascular system. Examples of symptoms of dysbiosis include nausea, diarrhea, and bloating.
Can you give an example of beta-, gamma- and epsilon-proteobacteria? What characteristics does each class of bacteria share?
beta- Betaproteobacteria are eutrophs meaning that they require a large amounts of organic nutrients. Betaproteobacteria can grow in aerobic and anaerobic areas such as mammal intestines, they are fastidious (difficult to culture) they require high levels of moisture, nutrient supplements, and carbon dioxide. They are distinctly microaerophilic, meaning that they require low levels of oxygen.
gamma- he most diverse class of gram-negative bacteria is Gammaproteobacteria. It contains about 250 genera, which makes it the most genus-rich taxon of the Prokaryotes. This category involves many widely recognized diseases/pathogens such as; Pseudomonaceae family, order Vibrionales which includes Vibrio cholerae, The genus Legionella which includes L. pneumophila, the pathogen responsible for Legionnaires disease.
epsilon- he smallest class of Proteobacteria is Epsilonproteobacteria. they are a microaerophilic bacteria, well known pathogens in this class are Campylobacter which can cause food poisoning . the genus Helicobacter is apart of the normal stomach microbiota, it can survive in stomach acid , however it’s also one of the leading causes of chronic gastritis and ulcers of the stomach and duodenum and has been known to be linked to stomach cancer.
One thing they all share is that all protobacteria are gram-negative.
What are spirochetes, and why are their flagella special? Give a couple of examples.
Spirochetes are any group of spiral shaped bacteria. They can be serious pathogens that cause diseases such as syphilis, yaws, lyme disease, and relapsing fever. Their motility is different than most bacteria because they have endoflagella (flagella is located in the periplasm, the inner space between the inner and outer membranes). The flagella rotates in the periplasm causing the entire cell to rotate / undulate, allowing the spirochetes to swim easily through gel-like materials that hinger other flagellated organisms.
Which bacteria are common components of probiotics such as yogurt (Look at your yogurt nutrition label for more information)?
Lactobacillus bulgaricus and Streptococcus thermophilus,also more types of lactobacilli and bifidobacteria may be added. The bacteria convert the sugar in milk to lactic acid.
Discuss the arguments FOR and AGAINST the classification of viruses as living organisms.
It’s a very weird argument between viruses being a living thing and a non living thing.
The argument for it being alive:
They reproduce,
they have nucleic acid
Adapt to surrounding
have organization.
However the arguments against the it being alive are:
They cannot reproduce without a host cell (They cannot reproduce by themselves)
Not made of organelles
don’t make their own energy
and don’t have cell process.
Define the word “tropism” and explain how a virus like polio can be transmitted by food or water, but cause disease in the nervous system.
Polio is an enteric virus, meaning it is primarily spread through the fecal-oral route. If polio is transmitted by contaminated food or water, how can it cause damage to the nervous system, and how is this related to the concept of “tropism”? There are two youtube videos linked at the bottom I found helpful.
Tropism is essentially a term for the affinity of a virus to infect only particular types of cells. For polio, these are intestinal epithelial cells and motor neurons in the central nervous system. Polio starts infecting the body in intestinal epithelial cells, which are eventually lysed and release replicated poliovirus. Many of those viruses continue passing through the GI tract where they might infect other hosts through the fecal-oral route. Others might find their way into the lymphatic system and then to the bloodstream. Once in the bloodstream, they are able to move all over the body. For only an unlucky few (about 1 in 100) the virus will actually pass the blood-brain barrier and infect motor neurons in the central nervous system, causing weakness, and in severe cases paralysis.
Tropism plays an important role in the prognosis of those infected with polio. Because polio only infects cells in the intestinal epithelium and the CNS, the majority of people (70%) don’t experience any symptoms. Even if the virus enters the bloodstream, there’s very little damage that can be done outside of the CNS. In some patients (29%), mild and brief flu-like symptoms can be experienced due to the body’s immune response. For the unlucky 1% in which polio spreads to the CNS, neurological symptoms can occur; however, the virus only causes neurological symptoms related to movement and motor coordination. Because polio has an affinity for motor neurons specifically, it doesn’t infect other neurons that might cause cognitive or sensory impairment.
What is the “envelope” of a viral envelope? Where does it come from and what features are uniquely viral?
The viral envelope is a layer on the outside part of the capsid of some viruses. The formation of the envelope happens when the virus is released from the cell, it takes part of the host membrane with it, and then replace the host proteins with viral proteins.
What are bacteriophages? What do they look like? How might a bacteriophage (a virus that infects bacteria) be used to treat bacterial infections in humans?
Bacteriophages are the viruses that infect bacteria. Bacteriophage is injected in humans who have a bacterial infection. The bacteriophage can infect and kill the bacteria leaving the beneficial bacteria of the normal microbiota untouched.
What are the lytic cycle and lysogenic cycle of phages? What is lysogenic conversion? What is a temperate phage?
Lytic Cycle:
Including 5 stages:
1.Attachement: The phage attaches to the surface of the host
2.Penetration: The viral DNA enters the host cell
3.Biosynthesis: Phage DNA replicates and phage proteins are made.
4.Maturation: New Phage particles are assembled.
5.Lysis: The cell lyses, releasing the newly made phages.
Lysogenic Cycle:
Including 7 stages:
1.The phage infects a cell
2.The phage DNA becomes incorporated into the host genome.
3.The cell divides, and prophage DNA is passed on to daughter cells.
4.Under stressful conditions, the prophage DNA is excised from the bacterial chromosome and enters the lytic cycle
5.Phage DNA replicates and phage proteins are made.
6.New Phage particles are assembled
7.The cell lyses, releasing the newly made phages.
Temperate phage is the ability of some bacteriophages to display a lysogenic life cycle. Many temperate phages can integrate their genomes into their host bacterium’s chromosome, together becoming a lysogen (a condition in which the host chromosome carries viral DNA) as the phage genome becomes a prophage. These phages can infect bacterial cell but rarely cause lysis.
Lysogenic conversion - when a bacterium acquires a new trait from its temperate phage. In lysogenic conversion, the phage inserts specific characteristics into the bacterial genes causing the bacteria to have better survival.
What is a latent virus infection? What is the relationship between chickenpox and shingles?
A latent virus infection is a viral infection that is dormant, or currently inactive. In this state, it no longer produces new viral phages, but stays in the host cells potentially for many years.
An example of this is the Varicella zoster virus; its primary infection causes the chickenpox early in life, but once this initial infection clears up, the virus can still reside in the nerve cells of the patient. Varicella zoster can become active later in the patient’s life, causing shingles.
Describe other noncellular infectious agents such as prion and viroids. Give some examples of prion diseases in humans and in animals.
Viroids are infectious entities that affect plants. They’re smaller than the smallest known virus and only contain 200-400 base pairs. They consist of only nucleic acid and are absent of a protein coat. Prions are infectious proteins that are misfolded and can transmit their misfolded shape to other functioning proteins. An example of prion disease in cattle is mad-cow disease and in humans, there is Creutzfeldt–Jakob disease, or CJD, a rapid neurodegenerative disease.
Do you know the evolutionary progression of MRSA? Briefly explain.
MRSA is a strain of s. aureus that has . developed a resistance to most antibiotics. MRSA is mostly spread from skin to skin contact but can also be spread from objects the infected individual has came into. MRSA undergoes genetic mutation which helps it to evolve in resistance
Know a few virulence factors of MRSA. How does protein A work?
Methicillin-resistant Staphylococcus aureus (MRSA) strains are very serious and can be potentially lethal pathogens that posses virulence mechanisms including toxins, adhesions, enzymes, and immunomodulators. One of these is Panton-Valentine leukocidin (PVL), a toxin associated with abscess formation and severe necrotizing pneumonia. Another one is phenol soluble modulins (PSMs), which are produced by most staphylocci and have the ability to attack human neutrophils (type of white blood cell).
Protein A interferes with the host’s B-cells within their immune system to prevent S. aureus from being phagocytosed and destroyed.
How are impetigo and SSSS different? What are the main toxins responsible?
SSSS mostly affects newborns and babies where exotoxins cause blisters and large scale skin peeling. Impetigo is a highly contagious condition commonly in children, where exotoxins cause peeling skin, crusty and flaky scabs around the mouth, face, and extremities.
What do the terms metabolism, catabolism and anabolism refer to?
Metabolism is the sum of both catabolism and anabolism. It refers to the total chemical reactions that are in living organisms.
Catabolism is the breaking down of larger molecules into smaller ones, such as glycolysis of carbohydrates.
Anabolism is the opposite, where it refers to the building up of larger molecules from smaller ones, such as synthesizing ribosomes.
How do we categorize organisms based on their carbon and energy sources?
Autotrophs: These organisms are able to synthesize their own organic compounds using inorganic carbon sources such as carbon dioxide (CO2). Autotrophs can be further divided into two types:
Photoautotrophs: These organisms use light as their energy source for photosynthesis. Examples include plants, algae, and cyanobacteria.
Chemoautotrophs: These organisms obtain energy from chemical reactions involving inorganic compounds, such as hydrogen sulfide (H2S) or ammonia (NH3). Examples include some bacteria and archaea.
Heterotrophs: These organisms obtain organic compounds and energy by consuming other organisms or organic matter. Heterotrophs can be further divided into two types:
Photoheterotrophs: These organisms use light as their energy source but cannot synthesize their own organic compounds. Instead, they obtain organic compounds from other organisms or the environment. Examples include some bacteria and algae.
Chemoheterotrophs: These organisms obtain both energy and organic compounds from other organisms or the environment. Examples include animals, fungi, and many bacteria.
What are redox reactions? Do you know who loses electrons and who gains them?
A redox reaction includes a reduction and an oxidation. The reducing agent LOSES electrons and reduces the other compound, while the oxidizing agent GAINS electrons and oxidizes the other compound. An example of a redox reaction is combustion.
What is the structure of ATP, and how does this make it a high energy molecule? What are activated carriers?
The structure of ATP is an Adenine molecule, a ribose molecule and three bonded phosphate groups. ATP is a high energy molecule because it provides energy that is stored between the second and third phosphate group. Activated carriers are small molecules that contain high energy bonds and energy can be easily exchangeable and some examples are ATP, NAD+ and NADPH.
How do enzymes work? What is the induced fit model?
Enzymes are biological catalysts that lowers a reaction’s activation energy. They help facilitate chemical reactions within the cell. They increase the rate of chemical reactions in the human body but does not create a reaction. They are essential for respiration, digestion, muscle and nerve functions.
The induced fit model is the active site of an enzyme the undergoes conformational change upon a substrate binding to be able to improve the fit.
What can you add to an “apoenzyme” to make it a “holoenzyme”? Name two different categories that fit this description!
An apoenzyme is an enzyme missing a cofactor or coenzyme that will allow it to be activated. Adding a cofactor (an inorganic ion) or coenzyme (an organic helper molecule) will change the shape of the enzyme allowing it to bind with its particular substrate and become activated. Holoenzymes are enzymes with their associated cofactors or coenzymes that allow them to be active and bind with a substrate so adding a cofactor or coenzyme would turn an apoenzyme into a holoenzyme. An example of a coenzyme is coenzyme a used in respiration as well as NADH and ATP.
One example of something that would also increase the effectiveness of an enzyme is an allosteric activator which binds to allocation on the enzyme away from the active site (where the reaction takes place) and changes the shape of the enzyme allowing the holoenzyme to bind with its substrates.
What is the difference between a competitive inhibitor and a non-competitive inhibitor? How do cells use non-competitive inhibition to regulate metabolic pathways?
Competitive inhibitors are inhibitors that compete with the substrate for the same enzyme whereas non-competitive inhibitors bind to an allosteric site of an enzyme, which changes the shape of the enzyme, thus disabling the enzyme. Cells use non-competitive inhibition to regulate metabolic pathways by setting the final product of the metabolic pathway as the non-competitive inhibitor. In the presence of sufficient final products, the metabolic pathway will be disabled and no more substrates will be made.
How many molecules of ATP, NADH, and pyruvate are formed by the end of glycolysis? What is substrate-level phosphorylation?
At the end of glycolysis, 2 ATP, 2 NADH, and 2 pyruvate are formed. Substrate-level phosphorylation is when a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. This usually occurs in the cytoplasm of cells during glycolysis and in the mitochondria during Krebs cycle.
What are the products of the transition reaction? How many NADH and FADH2 are produced in ONE TURN of the Kreb’s cycle? How many ATP are produced per NADH? FADH2? How many ATP are produced in one turn?
The transition reaction connects glycolysis to the citric acid (Krebs) cycle. The transition reaction converts the two molecules of the 3-carbon pyruvate from glycolysis (and other pathways) into two molecules of the
-2-carbon molecule acetyl Coenzyme A (acetyl-CoA) and
-2 molecules of carbon dioxide
One turn of Kreb’s cycle produces 3 NADH and 1 FADH2
The oxidation of one molecule of NADH thus leads to the synthesis of 2.5 molecules of ATP, whereas the oxidation of FADH2, which enters the electron transport chain at complex II, yields only 1.5 ATP molecules
About (30-32) ATP are produced in one turn (break down 1 glucose molecule)
If you have time, please check out the link below. It helped me to understanding the concept a little more. The length of video is about 15 minutes long.
As electrons are passed down the electron transport chain, their energy is used to do what? Use “gradient” and ATP-synthase in your answer! Define “proton motive force”. What is oxidative phosphorylation?
As electrons are passed down the electron transport chain their energy is used to concentrate Hydrogen in the inner membrane space of the mitochondria and pump protons across the membrane. They do this by using the gradient to drive ATP synthase and the synthesis of ATP from ADP and Pi. Proton motive force is a force that promotes the proton’s movement across membranes down their electrochemical potential.
How is anaerobic respiration different from aerobic (cellular) respiration?
Cellular respiration always begins with glycolysis, which can occur either in the absence or presence of oxygen. Cellular respiration that proceeds in the absence of oxygen is anaerobic respiration. Cellular respiration that proceeds in the presence of oxygen is aerobic respiration.
Do you know the locations of these metabolic pathways in prokaryotic vs. eukaryotic cells?
Prokaryotic cell:
Glycolysis - occurs in the cytoplasm
Krebs cycle - occurs in the matrix of mitochondria
Electron Transport Chain - happens across the plasma membrane
Eukaryotic cell:
Glycolysis - occurs in the cytoplasm
Krebs cycle - occurs in the cytoplasm
Electron Transport Chain - happens across the inner membrane of mitochondrion
What is the main purpose of fermentation, and why is it necessary? Describe two main types of fermentation. What are the starting materials and what are the products in both cases?
Fermentation allows glucose to be continuously broken down to make ATP due to the recycling of NADH to NAD+. (Without fermentation, the electron carrier would be full of electrons, the entire process would back up, and no ATP would be produced.)
There are two types of fermentation, alcoholic and lactic acid. Fermentation follows glycolysis in the absence of oxygen. Alcoholic fermentation produces ethanol, carbon dioxide, and NAD+. Lactic acid fermentation produces lactic acid (lactate) and NAD+.
What is bacterial cell division called? What is the sequence of events?
Bacterial cell division is called binary fission. There are four steps. Step 1 is when the parent cell uncoils and replicates its chromosome. During step 2, the parent cell grows larger, increases its cytoplasmic content, and the two strands of chromosomes migrate to opposite ends of the cell. Step 3 is when the parent cell elongates with a septum forming in the middle and separates the two chromosomes. During step 4, a new wall is formed and the cell splits at the center, making two new daughter cells.
Understand the four phases of a growth curve. When are bacteria most vulnerable to physical or chemical agents?
Lag phase: Newly inoculated cells are adjusting to their new environment, which represents a flat growth period.
Log phase (exponential growth): Cells are exponentially growing while nutrients are adequate. This phase is best for research work.
Stationary phase: Nutrients are depleting and waste is accumulating causing the number of cells being born and the number of cells dying to be at equal.
Death phase: Cells are dying at a exponential rate because of too much waste build up.
Bacteria most vulnerable to physical or chemical agents during the log phase.
What are some ways to analyze bacterial population size? List direct and indirect methods.
The use of light microscope to count the cell is called direct method, whereas using a spectrophotometer for the determination of activity of bacterial cell is called indirect method.
What kind of relationship do bacteria in a biofilm have? How do they communicate with each other?
Biofilms provide a protected environment for bacteria and helps bacteria with resisting things such as antibiotics. It helps bacteria thrive in harsh environments ultimately. I would say the relationship is one of commensalism because bacteria benefits, but the biofilm isn’t affected.
What are the different oxygen categories of microbes? Do you know the difference between facultative anaerobes and aerotolerant microbes?
Obligate aerobes : These microbes require oxygen for their survival and growth. They use oxygen in respiration to generate energy for cellular processes.
Obligate anaerobes: These microbes cannot tolerate oxygen and can only survive and grow in the absence of oxygen.
Facultative anaerobes: These microbes can survive and grow in the presence or absence of oxygen. They can use oxygen when it is available but can also switch to anaerobic metabolism when oxygen is limited.
Aerotolerant Anaerobes: These microbes do not use oxygen for respiration but can tolerate its presence. They generate energy through fermentation, which does not require oxygen
Microaerophiles: (“Goldilocks”) These microbes require low levels of oxygen for their survival and growth. They have adapted to live in environments where the oxygen concentration is lower than atmospheric levels. They require a minimum level of oxygen for growth, about 1%–10%, well below the 21% found in the atmosphere.
Facultative anaerobes can use fermentation or respiration, while aerotolerant anaerobes can only use fermentation.
What are the different pH categories? Do you know a few examples?
he different pH categories are: less than 7 pH are acidic, pH of 7 is neutral, and more than 7 pH is alkaline or basic. Examples include pure water ( pH 7), urine( pH 6), gastric acid( pH 1).
Which bacterium would theoretically be more likely to grow at refrigerator temperatures: a human intestinal pathogen or a soil-borne plant pathogen? Explain WHY!
Soil borne pathogens can grow in different temperatures depending on their environments so it would easily grow in a refrigerator temperature due to it being easy to adapt.
Explain how salt and sugar can act as a preservative. A complete answer will contain the words osmotic pressure.
Salt and sugar act as preservatives by creating a high osmotic pressure environment that is inhospitable to microorganisms. This inhibits their growth and prevents spoilage of food products.
A prokaryotic cell hitched a ride to Earth on a space shuttle from some unknown planet. The organism is a psychrophile, halophile, and an obligate aerobe. Based on the characteristics of the microbe, describe the conditions on the planet it came from.
Because the organism is a psychrophile, halophile, and an obligate aerobe, a lot can be determined about the conditions of the planet it came from. Because it is a psychrophile, we know it’s planet has relatively low temperatures (<20 degrees C). Because it is also a halophile, the environment of its home planet must have a really high salt or saline content. And because it’s an obligate aerobe, we know that there had to be the presence of oxygen on the planet.
How are complex media different from chemically defined media? Can you tell them apart by looking at the ingredients of a medium?
Complex media contain extracts and digests of yeasts, meat, or plants. The chemical composition is not known in complex media. Chemically defined media, however, has a known chemical composition and are usually composed of pure biochemicals off the shelf.
Since the differences between the two medias are due to chemical composition, it would not be possible to tell them apart just by looking at them through our normal eyes.
What are general purpose, enriched, selective and differential media? Give some examples of each.
General purpose media can be used to grow a broad spectrum of microorganisms. Some examples are nutrient agar (NA) and trypticase soy agar (TSA).
Enriched media contains nutrients or growth factors for growing fastidious microbes. Some examples are blood agar and chocolate agar.
Selective media contains ingredients to inhibit the growth of certain microbes in order to isolate a specific type of microorganism. Examples are MAC (MacConkey agar) and PEA (phenylethyl alcohol agar).
Differential media allows multiple organisms to grow but display difference in their growth, for example, color differences. Some examples of differential media include MSA (mannitol salt agar) and MAC (MacConkey agar).
