Module 3 Flashcards
What are the five major types of microbes
Viruses, bacteria, fungi, protists, algae
Edit major microbes
Explain what a virus does and what it is
These are the smallest and simplest biological entities. They are acellular, and the DNA/RNA is in a protein shell
A virus can’t do anything by itself, unless it meets a host cell. (Depends on host cell for replication/metabolism) (steals nutrients and utilises host cell machinery)
Many viruses cause disease in humans, animals and plants
Explain what a bacteria does and what it is
These are normally unicellular (prokaryotes). They are able to reproduce, independent of a host cell. They also have their own metabolism
They can function as primary producers and decomposers
Explain what a fungi does and what it is
They are normally large complex cells(eukaryotes), however they could also be single-celled.
They have a membrane bound nucleus, and contain complex organelles like mitochondria, golgi apparatus
Fungi are heterotrophs so they would have to absorb nutrients from external sources. And they could reproduce sexually or asexually
Fungi are primarily decomposers, breaking down dead organic material and recycling nutrients in ecosystems. Some fungi form symbiotic relationships with plants, helping them absorb nutrients
Explain what a protist does and what it is
Protists are a diverse group of mostly single-celled eukaryotic organisms, which means they have a nucleus and other organelles enclosed within membranes. Protists don’t fit neatly into other kingdoms like plants, animals, or fungi, so they are often considered a “catch-all” group for eukaryotes that don’t fall into these categories.
They can do various functions like decompose and photosynthesise, however many are also predators.
Explain what an algae does and what it is
Algae are a diverse group of primarily aquatic, photosynthetic organisms. They are similar to plants in that they contain chlorophyll and produce their own food through photosynthesis, but they lack many structural features of land plants, like roots, stems, and leaves. Algae are found in a wide range of environments, including freshwater, saltwater, damp soil, and even on rocks or in snow.
They can reproduce sexually or asexually
What are some key inventions and ideas in microbiology
Microscopes, agar plates, spontaneous generation, germ theory, Koch’s postulates, Penicillin
Who came up with the term ‘cells’
Robert Hooke came up with it in his book called “micrographia”
Who discovered bacteria and protists
Antonie van Leeuwenhoek in 1684 by using powerful microscopes (300x)
What did Louis Pasteur contribute to the field of microbiology
Developed vaccines
Developed the process of pasterusation
Fermentation
Disproved spontaneous generation
What was spontaneous generation
The belief that live organisms can be generated from non-living organisms, without the involvement of pre-existing life
I.e. believed that maggots came from rotting flesh (just like that - no other factor)
What was the ‘proof’ for spontaneous generation
John needham used broth that was boiled then sealed in flasks. Microorganisms then appeared in the broth of hay water, suggesting that life could spotaneously arise from broths
How was spontaneous generation challenged by Pasteur and Redi
Redi showed that maggots on meat came from fly eggs - not the meat itself
Pasteur conducted an experiment where he used a swan bottled flask to see if microorganisms could grow. Basically this swan bottled flask acted to stop bacteria from coming in from the air - provides air to the liquid, but prevents bacteria from getting in as they get stuck in the swan bottle neck. However, when the curved neck was removed, air could enter and bring microorganisms which grow in broth. This suggests that microbes in air was responsible for contamination
What was the germ theory of disease
Believed that microbes were the causative agents of disease (previously believed that it was miasma - bad air which caused disease)
germs are transmitted from one individual to another from contaminated surfaces etc
Koch’s postulates were an important aspect to this theory
What were Koch’s postulates for disease
An organism that causes a disease must:
Be able to be found in all organisms which have the disease
Be able to be isolated
The isolated organism should be able to be reintroduced to another organism and cause disease (i.e. produce disease in experimentally infected host)
Be reisolated from the experimentally infected host
What was penicillin
It was discovered by Alexander Fleming who found a random fungi (penicillium) who’s juices were able to kill bacteria. –> as well as many bacterias
Penicillin was mass produced by Florens and Chain from 1935-1945, which helped with WW2
How many lives did penicillin save
100 000 in WW2, and over 200 million lives since then
What else was Robert Koch well known for in his contributions to microbiology
He develped staining methods for microscopy
Use of solid growth medium (agar) which allowed for isolating colonies (which wasn’t achievable before)
We now use agar in everyday life
What are normal flora
These are normal microbes that live in us and on us, and dont normally cause disease for us
They are normally acquired at birth, from diet and environment
WHat are the benefits of a microbiota
Primes immune system
Improves digestion
Nutritional benefits
Competes with pathogens (for consumption of nutrients, which is good)
What are the drawbacks of microbiota
Potentially causing disease
Weakened immune system
Wrong location of microbiota could have negative impacts
Changes in conditions could cause microbiota to have a negative impact
What are pathogens ? What are the two types
These are disease causing microorganisms. The two types are obligate and opportunistic
What are obligate pathogens
These cause disease no matter the situation they are in (always cause disease)
What are opportunistic pathogens
These cause disease when optimal conditions arise. (i.e. under specific conditions)
What are some conditions which might be optimal for opportunistic pathogens
Temperature
Weakened immune system
Wrong location
Large numbers
Antiobiotic resistance
What is the concept of one health
Focusses on looking at health from a bigger picture
We need to consider animals, plants and environment when trying to manage human viruses
In other words, its encouraging us to consider the environmental origins of disease as well
Influence of urbanisation, globalisation, climate change etc.
Describe a major problematic infectious disease
Mycobacterium tuberculosis
This bacterium causes tuberculosis. Spreads person-to-person by airbone droplets such as coughing. It infects the lungs, causing cough, chest pain, weight loss and potentially death
Could be latent for many years, and approx 1/3 of the worlds population is infected
There is a large infection rate in Africa and SEA due to lack of medical facilities
What are the steps involved in food production
Production (i.e. initial natural production of food such as animals, plants etc) –> processing (actually processing the natural produce into something edible)–> distribution –> retail/restaurant –> Consumer
Explain how microbes could benefit the production stage
Rumen microbes help cows digest grass
Some fungi act as symbiotes to boost plant growth
Some microbes are useful for maintaining soil health (recycling wastes into nutrients)
Explain how microbes could benefit the processing stage
Microbes are needed for some processing, especially with the need for fermentation
Explain how microbes could benefit the retail/restaurant stage
Some microbes act as food sources in retail such as some fungi (mushrooms), algae
Explain how microbes could benefit the consumer stage
Boosting consumer/peoples gut microbiomes
Explain how microbes could have a detrimental impact on the production stage
Pathogens could kill animals and plants are cause diseases which could be passed on to humans
Post harvest contamination can ruin crops
irrigation water could be contaminated with pathogens
Explain how microbes could have a detrimental impact on the processing stage
Factories could be contaminated with microbes, having a negative impact
Explain how microbes could have a detrimental impact on the distribution stage
Refrigeration needed to stop microbial growth
Explain how microbes could have a detrimental impact on the retail/restaurant stage
Poor hygiene can result in microbial growth on food
Explain how microbes could have a detrimental impact on the consumer stage
Poor gut microbiota causes poor health (controlled by what we eat)
How can microbes enhance food production in plants
They can help fix nitrogen (which is necessary to maintain good health)
Kill animal and plant pathogens
Break down organic wastes into inorganic nutrients
Breaks down toxins e.g. pesticides
How can microbes enhance food production in animals
The cellulose in plants is thick and thus hard to digest. However, rumen microbes are able to help with the digestion here, to turn cellulose into sugars and organic acids
What is mutualism
Both organisms benefit
What are examples of useful mutualistic relationships
Mycorrhizal fungi, rhizobium bacteria
How can mycorrhizal fungi have a beneficial impact
Mycorrhizal fungi are in most plants roots , and they help enhance water and inorganic nutrient uptake, and receive sugars from the plants in return
how can rhizobium bacteria have a beneficial impact
Rhizobium bacteria are in legume roots
They help fix nitrogen (i.e. turn N2 in air to nitrogen (ammonia) that the plants can use). They also receive sugars in return
What are pathogens
Organisms causing disease
Explain plant pathogens - examples and whats happened
Crop pathogens cause global losses of ~30% total yield (~1 trillion USD) - a big one impacts is the tobacco mosaic virus
When we have monocoultures, the probability of pathogens affecting the plant species is great (in this caase, it is when the species have the same gene). The Sigatoka fungi threatened the survival of cavendish bananas because they were genetically identical –> all equally susceptible to the fungi –. almost caused their extinction
Explain the extent and nature of animal pathogens
Pathogens infecting animals inffect suffering, death and massive economic losses (~20% of total production)
These can exist in viruses, vacteria, fungi or protists
What are examples of animal pathogens
Foot and Mouth Disease Virus
Salmonella spp
Bovine tuberculosis
Avian Influenza virus
Explain foot and mouth disease
Not in Aus
Contagious viral disease affecting cattle, pigs, sheep, goats and other cloven-hoofed animals
Causes fevers, blisters and lameness –> decreased milk and meat
Explain salmonella
In Aus but controllable
Bactierla pathogen that affects a wide range of farm animals, and can causeIn Aus but controllable
Bactierla pathogen that affects a wide range of farm animals, and can cause GI illness and is a major safety concern
Explain bovine tuberculosis
Bacterial infection affecting cattle and other animals, including deer and goats
Chronic disease can lead to respiratory issues and weight loss. Could be transmitted to humans
Explain avian influenza virus
Viral infection affecting poultry
Can cause sudden death, respiratory distress, decreased egg production –> economic impacts
What is zoonosis
This is when an animal carries a disease and transfers it to a human
Refers to human infections arising from animals. Microbes could be pathogenic to both animals and human hosts or could be normal flora for animals but harmful for humans
Animal is a ‘vector’ for disease
What is a ‘vector’
Something that transmits a pathogen
Explain the rolle of fermentation in food production
It has multiple meanings such as; microbial transformation of foods by fungi or bacteria or anaerobic metabolism of sugars –> alcohols, acids, CO2
Fermentation is a metabolic process in which microorganisms like bacteria, yeast, or molds convert sugars (carbohydrates) into acids, gases, or alcohol. In food production, fermentation plays a critical role in enhancing flavor, texture, preservation, and nutritional value.
What are examples of fermentation in food production
Beer, bread, yoghurt, pickles, wine, kimchi and cheese
Explain fermentation in beer
Barley is used as a source of sugars to support fermentation, and the Hops is a natural preservative to provide bitterness, followed by Yeast which ferments sugars to alcohol and CO2.
What is food spoilage
This is where microbes such as fungi or bacteria grow on food. However, in most cases, this food isn’t poisonous
How could food spoilage be prevented
Refrigeration: cold enviro not conducive to microbial growth (
Preservations: chemical additions might kill microbes (Chemicals could have a harmful effect on us, also microbes could become tolerant –> bad for us)
fermentation: acidic environment (some microbes can survive in acidic environments)
What is food poisoning
Food poisoning occurs when food is contaminated with harmful microorganisms (bacteria, viruses, parasites) or their toxins, leading to illness when consumed. It is caused by eating food that contains pathogens or toxic substances that harm the digestive system or other parts of the body.
Thus, spoilage is not necessarily poisoning
What is food borne infection vs food borne intoxication?
Food borne infection is when microbes grow on foods when they aren’t meant to
meanwhile, food borne intoxication is when the microbes growing on foods are pathogenic or produce toxins which are harmful
What are the risk factors for food poisoning
Origins of food (determines types and numbers of microbes)
Storage and prep (refrigerated? raw/cooked?)
Human factors (hygiene)
Explain the concept of one health in food production
Maintaining a safe food supply depends on managing microbes at every stage oof the production chain
Soils, people, plants, factories, animals, kitchen
How does gut microbiome depend on diet
High fibre diet = bacteriodetes (good bacteria)
High fat and protein diet = firmicutes (bad bacteria)
We need a balance of both, but better to have more bacteriodetes
How does gut microbiome influence us
Healthy microbiome important for proper food digestion, reistance to pathogens , immune functions
Bad microbiome linked to allergies, T2 diabetes, cancer, obesity etc
What are the four laws of ecology
Everything is connected
Everything must go somewhere
There is no such thing as a free lunch
Nature knows best (i.e. evolution will always bring us to a balanced state)
What are autotrophs
Autotrophs describe organisms who can produce their own food, given certain energy sources such as CO2
Many use light and Chemical energy sources as fuel \
They convert inorganic C to organic C, acting as a ‘sink’ for CO2 –> acts to limit climate change
Autotrophs act as a carbon sink
What are the types of autotrophs we study
Chemotrophs (chemical energy sources) –> methanogens
Phototrophs (light energy sources)
What are methanogens? What is its impact on the environment
These are organisms which consume CO2 and H2 which produces methane
However, CH4 is actually very deterimental for the environment. As such, it has an overall negative impact despite consuming CO2. (Sink for CO2 but CH4 source which is bad)
They are largely anaerobic, so they are in oxygen-free habitats like deep sediments, soil micro-niches, animal gut
What actually does most of the photosynthesis in the world
Algae blooms perform 50% of photosynthesis –> really helpful
What are heterotrophs
These are organisms which must consume other organisms for food/energy. A major example of this is a methanotroph
What do methanotrophs do? What is its impact
These consume CH4 and produce CO2 as a result. Although it is argued that release of CO2 is bad, it can address CH4 levels rising, thus being very good.
Also, it could attack toxic pollutants such as trichloroethylene –> ebven more beneficial for environment
What are decomposers? Example?
Key group of heterotrophs which recycle dead cells and materials back to CO2 (i.e. recycling nutrients into simpler compounds)
Fungi are major decomposers in terrestial ecosystems
What are preadtors
These consume other microbes, and may pose a threat to other microbes. Preadotrs could include flagellates and ameobae
Typically, protists are predators,
Explain how heterotrophs can be pollutant degraders
Methanotrophs are one example of bacteria growing on hydrocarbons as their energy and carbon source.
Hydrocarbon degrading bacteria can be good for bioremediation - cleanup of poollution by microbes
They are heterotrophs specialising in eating ancient fossilised organic compounds
Similar to decomposers, but contain enzymes which attack hydrocarbons –> useful in cleaning pollutatns
Need to find more to help beneft the environment
Explain the coral symbiosis
The algae consumes CO2 and light to photosynthesise and produce sugars (which are then used by coral)
the coral utilises the sugars to produce CO2 as well
Thus, the cycle continues
Explain the lichen symbiosis
Lichens are primary producers of organic carbon in some habitats.
They are photosynthetic, but aern’t plants. they are actually a symbiosis between a heterotrophic fungus and an autotrophic algae.
The autotrophic algae takes carbon / CO2, and transforms it into sugar. This sugar is used by fungus to produce CO2, and the cycle continues. The fungus also provides physical protection
WHat is DNA cloning
It is a molecular biology technique used to create identical copies of a specific DNA fragment
Involves isolating and replicating a segment of DNA
WHat is recombinant DNA
Refers to a DNA molecule which has been artificially created by combining genetic material from different sources
What is GMO
Organism whose genetic material has been altered using genetic engineering techniques
Why are microbes useful for biotechnology (such as fungi and bacteria)
They could grow rapidlyy, have high genetic manipulability, which allows for ‘testing’ of various genetics (
This is very important for research and industrial applications
Biotechnology is technology that utilizes biological systems, living organisms or parts of this to develop or create different products.
Why should we care about biotechnology
Plays a role in:
Food, drink, medication, agriculture, fuel, cleaning
What is biotechnology
It is where we use biology to help create a product:
Two types; cellular biotechnology and molecular biotechnology
What is cellular biotechnology
Cellular biotechnology involves the use of living cells to produce biological products, conduct research, or solve problems. It focuses on understanding and manipulating cell processes for various purposes.
What is molecular biotechnology
Molecular biotechnology focuses on manipulating DNA, RNA, proteins, and other molecules within cells to develop products or solve problems. It involves techniques such as gene cloning, genetic modification, and molecular analysis.
What microbes can be used for biotechnology
Typically virus and bacteria, but could also use Archaea, algae and fungi
Explain archaea as biotechnology
They have diverse living conditions
Source of enzymes (PCR, thermostable polymerases for copying DNA sequences)
Explain Algae as biotechnology
Green biotech –> good at making biofuels like H2 and ethanol
Converts CO2 and light into those biofuels
Low maintenance
Explain virus as biotechnology
Good at infecting a host cell, and using the host cell to make proteins and reproduce.
They can act as vectors to carry genes –> allowing a foreign gene to be transported to certain cells via viruses
Explain fungi as biotechnology
Yeasts - excellent cloning and expression hosts, similar to bacterial systems
Moulds - antibiotic synthesis, penicillin
Explain bacteria as biotechnology
Hosts for cloning DNA, expressing proteins. They are also easy and quick to work with
Explain why bacteria is normally used as a host cell
Fastest growth (20 minutes)
Very easy to extract and add plasmid DNA
We normally use E.coli as the ideal bacteria
WHat microbes are normally used as host cells
Bacteria and fungi/yeast
Explain why E.coli is the model organism for a host cell as a bacteria
Fast growth rate
Simple and well known genetics –> easy to manipulate
Low cost cultivation
Efficient plasmid propagation
Explain why fungi/yeast are normally used as a host cell
They express eukaryotic genes. This makes it good for application to humans, as the products produced by it will be suitable for human use, compared to bacteria which would only provide prokaryotic suitable products
We normally use cerevisae as the biotech here
Explain why cerevisae is normally used as a host cell
Because it is easy to cultivate, has rapid growth and relatively well known genetics
Good as it is a eukaryote as well –> similar to human cells, especially as many proteins need post-translational modifications to be functional. Thus, this could modify the products in was that the bacteria can’t, and make sure products are able to be used by humans
What are vectors
Any vehicle used to carry foreign genetic material into a host cell for replication or expression
What are plasmids
These are circular DNA elements found in microbes which replicate independently of the chromosome
Most commonly used vector
What are plasmids
These are small, circular, double stranded DNA molecules existing independently of the chromosomal DNA in bacteria and some eukaryotes
They have their own origin of replication, thus not relying on cell’s divison cycle
These aren’t necessary to survival of bacteria, however they can provide additional capabilities such as antibiotic resistance.
They are naturally found, and allow genes to be transferred
What are the key features of plasmid
Selectable (gene) marker
Replication function
Cloning site
What does a selectable (gene) marker do
Forces plasmid uptake into a bacteria (?!)
This could allow for antibiotic resistance or change in metabolic activity
What does a replication function do
Allows for the persistence of a plasmid in a host
What does a cloning site do
It is the site of manipulation, where we could insert foreign genes. It exposes an ‘easy gene’ to access
How can we clone molecules
We can either create identical organisms (GMO) OR make copies of a piece of DNA by adding it into a plasmid, then replicating the plasmid
What are the steps involved with doing plasmid replication (?!)
Recombinant DNA preparation (whart part is modified)
Transformation and screening (actually modifying the plasmid)
Copying and expressing
Explain the recombinant DNA preparation stage
Foreign DNA and plasmid vector are mixed together to form a recombinant DNA
We then identify the gene of interest, and digest a DNA (cut DNA) with restriction enzymes
We then ligate the DNA (Join the foreign DNA with vector) using a T4 ligase
Explain the transformation and screening stage
Transformation: Host cell to pick up recombinant DNA. To do this, we need to stimulate stressful conditions to cause it to want to pick up
We then use a selectable gene marker to verify successful cloning by monitoring the gene marker
Screening: Once the recombinant plasmid is inside the host cell, not all cells will have successfully taken up the plasmid or integrated the desired gene. Therefore, screening is necessary to identify cells that have the recombinant DNA:
Explain the copying and expressing stage
Bacterial growth: After transformation, bacteria are cultured in liquid media. The cells divide and replicate the plasmid, which contains the recombinant DNA. This process results in the amplification (copying) of the plasmid and the inserted gene.
Plasmid replication: The plasmid has its own origin of replication, allowing it to independently replicate within the host cell, producing many copies of the recombinant DNA.
Gene expression: If the goal is to produce a protein from the inserted gene, the gene needs to be expressed (transcribed and translated into protein). This often requires an appropriate promoter sequence (often derived from viruses or bacteria) that drives transcription of the gene in the host cell.
Or it could be expressed in an end product such as HepB vaccine or used to make another product (enzymes, soure of algal biofuels as well)
Ultimately, the result is a GMO with a foreign gene
Why are vaccines important
They are important as they can save lives
They can protect against a variety of diseases such as smallpox, polio, ravies etc
Some diseases have no cure, so prevention through vaccines is the only option
They allow for ‘herd immunity’
How do vaccines work
Vaccines work on the adaptive immune system, and how it can recognise antigens associated with a pathogen
They basically consist of live (weakened) microbes, dead microbes, antigens produced of pathogens etc, and get the body used to how they are going to respond
How can a recombinant vaccine be produced (with HepB vaccine as an example)
1) Recombinant DNA preparation:
Identify gene of interest (surface protein antigen HBAg). This gene is digested and then ligated through a yeast plasmid vector.
2) Transformation and screening:
Transformation into yeast host, and then select those which were actually successful in transofmring
3) Copying and expressing
See whether the recombinant yeast actually expresses foreign gene, and then purify it to make an antigen product; which in this case is the HepB vaccine
