Module 3 Flashcards

1
Q

What are the five major types of microbes

A

Viruses, bacteria, fungi, protists, algae

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2
Q

Edit major microbes

A
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3
Q

Explain what a virus does and what it is

A

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

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4
Q

Explain what a bacteria does and what it is

A

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

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5
Q

Explain what a fungi does and what it is

A

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

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6
Q

Explain what a protist does and what it is

A

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.

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7
Q

Explain what an algae does and what it is

A

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

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8
Q

What are some key inventions and ideas in microbiology

A

Microscopes, agar plates, spontaneous generation, germ theory, Koch’s postulates, Penicillin

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9
Q

Who came up with the term ‘cells’

A

Robert Hooke came up with it in his book called “micrographia”

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10
Q

Who discovered bacteria and protists

A

Antonie van Leeuwenhoek in 1684 by using powerful microscopes (300x)

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11
Q

What did Louis Pasteur contribute to the field of microbiology

A

Developed vaccines

Developed the process of pasterusation

Fermentation

Disproved spontaneous generation

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12
Q

What was spontaneous generation

A

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)

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13
Q

What was the ‘proof’ for spontaneous generation

A

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

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14
Q

How was spontaneous generation challenged by Pasteur and Redi

A

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

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15
Q

What was the germ theory of disease

A

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

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16
Q

What were Koch’s postulates for disease

A

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

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17
Q

What was penicillin

A

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

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18
Q

How many lives did penicillin save

A

100 000 in WW2, and over 200 million lives since then

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19
Q

What else was Robert Koch well known for in his contributions to microbiology

A

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

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20
Q

What are normal flora

A

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

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21
Q

WHat are the benefits of a microbiota

A

Primes immune system

Improves digestion

Nutritional benefits

Competes with pathogens (for consumption of nutrients, which is good)

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22
Q

What are the drawbacks of microbiota

A

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

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23
Q

What are pathogens ? What are the two types

A

These are disease causing microorganisms. The two types are obligate and opportunistic

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24
Q

What are obligate pathogens

A

These cause disease no matter the situation they are in (always cause disease)

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25
Q

What are opportunistic pathogens

A

These cause disease when optimal conditions arise. (i.e. under specific conditions)

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26
Q

What are some conditions which might be optimal for opportunistic pathogens

A

Temperature

Weakened immune system

Wrong location

Large numbers

Antiobiotic resistance

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27
Q

What is the concept of one health

A

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.

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28
Q

Describe a major problematic infectious disease

A

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

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29
Q

What are the steps involved in food production

A

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

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30
Q

Explain how microbes could benefit the production stage

A

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)

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31
Q

Explain how microbes could benefit the processing stage

A

Microbes are needed for some processing, especially with the need for fermentation

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32
Q

Explain how microbes could benefit the retail/restaurant stage

A

Some microbes act as food sources in retail such as some fungi (mushrooms), algae

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33
Q

Explain how microbes could benefit the consumer stage

A

Boosting consumer/peoples gut microbiomes

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34
Q

Explain how microbes could have a detrimental impact on the production stage

A

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

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35
Q

Explain how microbes could have a detrimental impact on the processing stage

A

Factories could be contaminated with microbes, having a negative impact

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36
Q

Explain how microbes could have a detrimental impact on the distribution stage

A

Refrigeration needed to stop microbial growth

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37
Q

Explain how microbes could have a detrimental impact on the retail/restaurant stage

A

Poor hygiene can result in microbial growth on food

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38
Q

Explain how microbes could have a detrimental impact on the consumer stage

A

Poor gut microbiota causes poor health (controlled by what we eat)

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39
Q

How can microbes enhance food production in plants

A

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

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40
Q

How can microbes enhance food production in animals

A

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

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41
Q

What is mutualism

A

Both organisms benefit

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42
Q

What are examples of useful mutualistic relationships

A

Mycorrhizal fungi, rhizobium bacteria

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43
Q

How can mycorrhizal fungi have a beneficial impact

A

Mycorrhizal fungi are in most plants roots , and they help enhance water and inorganic nutrient uptake, and receive sugars from the plants in return

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44
Q

how can rhizobium bacteria have a beneficial impact

A

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

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45
Q

What are pathogens

A

Organisms causing disease

46
Q

Explain plant pathogens - examples and whats happened

A

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

47
Q

Explain the extent and nature of animal pathogens

A

Pathogens infecting animals inffect suffering, death and massive economic losses (~20% of total production)

These can exist in viruses, vacteria, fungi or protists

48
Q

What are examples of animal pathogens

A

Foot and Mouth Disease Virus

Salmonella spp

Bovine tuberculosis

Avian Influenza virus

49
Q

Explain foot and mouth disease

A

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

50
Q

Explain salmonella

A

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

51
Q

Explain bovine tuberculosis

A

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

52
Q

Explain avian influenza virus

A

Viral infection affecting poultry

Can cause sudden death, respiratory distress, decreased egg production –> economic impacts

53
Q

What is zoonosis

A

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

54
Q

What is a ‘vector’

A

Something that transmits a pathogen

55
Q

Explain the rolle of fermentation in food production

A

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.

56
Q

What are examples of fermentation in food production

A

Beer, bread, yoghurt, pickles, wine, kimchi and cheese

57
Q

Explain fermentation in beer

A

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.

58
Q

What is food spoilage

A

This is where microbes such as fungi or bacteria grow on food. However, in most cases, this food isn’t poisonous

59
Q

How could food spoilage be prevented

A

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)

60
Q

What is food poisoning

A

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

61
Q

What is food borne infection vs food borne intoxication?

A

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

62
Q

What are the risk factors for food poisoning

A

Origins of food (determines types and numbers of microbes)

Storage and prep (refrigerated? raw/cooked?)

Human factors (hygiene)

63
Q

Explain the concept of one health in food production

A

Maintaining a safe food supply depends on managing microbes at every stage oof the production chain

Soils, people, plants, factories, animals, kitchen

64
Q

How does gut microbiome depend on diet

A

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

65
Q

How does gut microbiome influence us

A

Healthy microbiome important for proper food digestion, reistance to pathogens , immune functions

Bad microbiome linked to allergies, T2 diabetes, cancer, obesity etc

66
Q

What are the four laws of ecology

A

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)

67
Q

What are autotrophs

A

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

68
Q

What are the types of autotrophs we study

A

Chemotrophs (chemical energy sources) –> methanogens

Phototrophs (light energy sources)

69
Q

What are methanogens? What is its impact on the environment

A

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

70
Q

What actually does most of the photosynthesis in the world

A

Algae blooms perform 50% of photosynthesis –> really helpful

71
Q

What are heterotrophs

A

These are organisms which must consume other organisms for food/energy. A major example of this is a methanotroph

72
Q

What do methanotrophs do? What is its impact

A

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

73
Q

What are decomposers? Example?

A

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

74
Q

What are preadtors

A

These consume other microbes, and may pose a threat to other microbes. Preadotrs could include flagellates and ameobae

Typically, protists are predators,

75
Q

Explain how heterotrophs can be pollutant degraders

A

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

76
Q

Explain the coral symbiosis

A

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

77
Q

Explain the lichen symbiosis

A

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

78
Q

WHat is DNA cloning

A

It is a molecular biology technique used to create identical copies of a specific DNA fragment

Involves isolating and replicating a segment of DNA

79
Q

WHat is recombinant DNA

A

Refers to a DNA molecule which has been artificially created by combining genetic material from different sources

80
Q

What is GMO

A

Organism whose genetic material has been altered using genetic engineering techniques

81
Q

Why are microbes useful for biotechnology (such as fungi and bacteria)

A

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.

82
Q

Why should we care about biotechnology

A

Plays a role in:

Food, drink, medication, agriculture, fuel, cleaning

83
Q

What is biotechnology

A

It is where we use biology to help create a product:

Two types; cellular biotechnology and molecular biotechnology

84
Q

What is cellular biotechnology

A

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.

85
Q

What is molecular biotechnology

A

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.

86
Q

What microbes can be used for biotechnology

A

Typically virus and bacteria, but could also use Archaea, algae and fungi

87
Q

Explain archaea as biotechnology

A

They have diverse living conditions

Source of enzymes (PCR, thermostable polymerases for copying DNA sequences)

88
Q

Explain Algae as biotechnology

A

Green biotech –> good at making biofuels like H2 and ethanol

Converts CO2 and light into those biofuels

Low maintenance

89
Q

Explain virus as biotechnology

A

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

90
Q

Explain fungi as biotechnology

A

Yeasts - excellent cloning and expression hosts, similar to bacterial systems

Moulds - antibiotic synthesis, penicillin

91
Q

Explain bacteria as biotechnology

A

Hosts for cloning DNA, expressing proteins. They are also easy and quick to work with

92
Q

Explain why bacteria is normally used as a host cell

A

Fastest growth (20 minutes)

Very easy to extract and add plasmid DNA

We normally use E.coli as the ideal bacteria

93
Q

WHat microbes are normally used as host cells

A

Bacteria and fungi/yeast

94
Q

Explain why E.coli is the model organism for a host cell as a bacteria

A

Fast growth rate

Simple and well known genetics –> easy to manipulate

Low cost cultivation

Efficient plasmid propagation

95
Q

Explain why fungi/yeast are normally used as a host cell

A

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

96
Q

Explain why cerevisae is normally used as a host cell

A

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

97
Q

What are vectors

A

Any vehicle used to carry foreign genetic material into a host cell for replication or expression

98
Q

What are plasmids

A

These are circular DNA elements found in microbes which replicate independently of the chromosome

Most commonly used vector

99
Q

What are plasmids

A

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

100
Q

What are the key features of plasmid

A

Selectable (gene) marker

Replication function

Cloning site

101
Q

What does a selectable (gene) marker do

A

Forces plasmid uptake into a bacteria (?!)

This could allow for antibiotic resistance or change in metabolic activity

102
Q

What does a replication function do

A

Allows for the persistence of a plasmid in a host

103
Q

What does a cloning site do

A

It is the site of manipulation, where we could insert foreign genes. It exposes an ‘easy gene’ to access

104
Q

How can we clone molecules

A

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

105
Q

What are the steps involved with doing plasmid replication (?!)

A

Recombinant DNA preparation (whart part is modified)

Transformation and screening (actually modifying the plasmid)

Copying and expressing

106
Q

Explain the recombinant DNA preparation stage

A

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

107
Q

Explain the transformation and screening stage

A

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:

108
Q

Explain the copying and expressing stage

A

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

109
Q

Why are vaccines important

A

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’

110
Q

How do vaccines work

A

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

111
Q

How can a recombinant vaccine be produced (with HepB vaccine as an example)

A

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

112
Q
A