Unit 1: Biotechnology and GM Foods

I. Biotechnology

• Biotechnology involves using technology to develop and alter living organisms to meet the demands of our growing population. Cloning and genetic modification exemplify biotechnological techniques, which find application in various sectors, including food production.

1. Yeast and bread

• Yeast, a type of fungi, plays a crucial role in breadmaking.

• The process involves the breakdown of carbohydrates in flour by enzymes, leading to sugar formation.

• Subsequently, yeast undergoes aerobic respiration, producing carbon dioxide.

• As oxygen depletes, yeast switches to anaerobic respiration, generating ethanol and more carbon dioxide, causing the dough to rise.

• Baking kills the yeast, halting the rising process but leaving air pockets in the bread.

2. Bacteria and Yoghurt

• Bacteria fermentation of milk produces yoghurt.

• Pasteurization, heating milk to kill harmful microorganisms, is followed by the addition of Lactobacillus bacteria.

• Fermentation by these bacteria leads to the production of lactic acid, which solidifies the milk into yoghurt.

3. Lactase and Lactose-Free Milk

• Lactose, present in milk, is broken down by the enzyme lactase. Individuals lacking lactase experience lactose intolerance. Adding lactase to milk facilitates the breakdown of lactose into glucose and galactose, producing lactose-free milk.

II. Other Examples of Biotechnology

1. Pectinase in Fruit Juice Production

• Pectinase, an enzyme from fungi and bacteria, aids in breaking down pectin in plant cell walls during fruit and vegetable processing, facilitating juice extraction.

2. Enzymes in Biological Washing Powders

• Enzymes in biological washing powders enhance stain removal at lower temperatures compared to non-biological alternatives.

3. Yeast in Biofuel Production

• Yeast fermentation of biomass sugars produces ethanol, utilized as a biofuel.

4. Penicillium for Penicillin Production

• Penicillium fungus is mass-cultivated in industrial fermenters to produce penicillin, a widely-used antibiotic, under controlled conditions.

III. Genetically Modified Organisms (GMOs)

1. Transgenic Organisms

• Transgenic organisms incorporate genes from other species, altering their genetic makeup.

2. Insulin Production by GMOs

• Genetically modified organisms, such as E. coli, are utilized to produce insulin, necessitating purification for human use.

3. GMOs in Food Production

• Genetically modified organisms, like modified Fusarium fungus, can yield high-protein supplements like mycoprotein for vegetarians, cultivated under controlled conditions.

4. Golden Rice

• Golden rice, a genetically modified variant, offers enhanced nutritional value.

5. Crop Resistance

• GMOs can confer resistance to insects and pesticides in crops, thereby increasing yield.

Unit 2: Classification

I. Definition

• Living organisms are classified to facilitate comparison and highlight differences. Classification systems aim to reflect evolutionary relationships, grouping organisms based on shared features.

• Classification in biology organizes organisms based on characteristics and evolutionary relationships, aiding study and communication.

• Classification aids conservation efforts by providing insights into species relationships and ecological roles, helping prioritize conservation measures.

• Taxonomy, closely related to classification, encompasses description, identification, and naming of species.

1. Kingdom

• Organisms are categorized into five kingdoms:

  • Plants, animals, fungi, protists, and prokaryotes. Examples include Plasmodium and Amoeba for protists, and bacteria like Staphylococcus aureus for prokaryotes.

2. Phylum

• Phylum is a classification between Kingdom and Class, generalized based on organism body plans. For instance, humans belong to the Chordata class.

3. Class

• Organisms are further divided into classes, such as mammals, fish, reptiles, and birds.

4. Order

• Orders of organisms are defined after classes, like bats, carnivores, and rodents within mammals.

5. Family

• Families, subdivisions of classes, group organisms further, e.g., pigeons and doves, ducks within birds.

6. Genus

• Families are divided into genera, for instance, Felix for domestic cats.

7. Species

• Species represent the final division, defined as groups capable of reproducing fertile offspring.

II. Overview

• The binomial system, utilizing genus and species, is internationally adopted for naming organisms. Key points include:

  • No overlap between groups.

  • Higher groups encompass more organisms.

  • Lower groups indicate closer relatedness.

  • The system undergoes continuous updates with new discoveries like gene sequencing.

III. Importance of Technological Developments

• Advancements in technology, like microscopes and chemical analysis, have revolutionized classification:

  • Microscopes aid in discerning organism differences, enhancing understanding.

  • Chemical analysis, including DNA sequencing, enables more accurate classification.

  • Carl Woese's 'three-domain system' categorizes organisms into Archea, Bacteria, and Eukaryota, based on RNA analysis.

  • Evolutionary trees depict species relationships, incorporating both current and fossil data.

• The ‘three-domain system’ involves dividing organisms into three categories:

1. Archea

• Archea are more primitive bacteria that have become accustomed to living in extreme environments. They have no nucleus. Examples include the halobacteriales.

2. Bacteria

• Bacteria cells are the true bacterial cells. They are again prokaryotic and examples include the Spirochates.

3. Eukaryota

• Eukaryota encompass the rest of the organisms. It includes fungi, plants, animals and protists. Anything with a membrane bound nucleus fits into this section.

4. Evolutionary Trees

a. Evolutionary trees show how organisms are related

• Evolutionary trees show the relationships between species. Living organisms are mapped using current data, however fossils are used to map extinct organisms. These trees therefore span generations upon generation and show how extinct organisms are linked to living organisms.

Unit 3: Fossils and Evolution

I. Definition

• Fossils can also be used to prove evolution.

• Fossils can be used to for dating and to record time. They give us a lot of evolutionary data.

II. Fossils can corroborate Darwin’s Theory of Evolution by Natural Selection

• As seen in Darwin’s theory of evolution, simple life forms developed into more complex ones. This can be seen in fossils, as the fossils of simpler organisms are found in older rocks, whereas the fossils of more complex organisms are found in newer rocks.

III. There are issues finding information on the oldest life forms

• Some of the oldest life forms had soft body forms. This means that there was very little else left behind over time. Geological activity, such as tectonic plate movement and earthquakes have destroyed the majority these fossils.

• By watching the developments of fossils over time and comparing and contrasting their ages, scientists can track the development of life over time. This is difficult and involves conjecture, however can be used to get a brief understanding of development, pending further research.

IV. Human Evolution and Fossils

• Fossils can also tells us about human evolution. Their evidence suggests that humans and chimpanzees come from a common ancestor.

1. Hominids

• The name for humans and their ancestors and fossils of different hominid species have been discovered. These fossils help us see how humans have evolved over time and they have characteristics that are somewhere between humans and apes:

a. A 4.4 million years old fossil hominid called ‘Ardi’

• This is a fossil of the species Ardipithecus ramidus which was found in Ethiopia. The fossil showed she had the following characteristics:

  • Brain size was similar to chimpanzees

  • Short legs but long arms like apes

  • Feet structure suggested she climbed trees

  • However, leg structure showed she walked upright without using her hands (which apes use)

b. A 3.2 million years old fossil hominid called ‘Lucy’

• This is a fossil of the species Australopithecus afarensis which was also found in Ethiopia. The fossil showed she was more similar to humans than Ardi:

  • Brain size slightly larger than Ardi’s

  • Arm and leg sizes were in the middle of what you’d find in humans and apes

  • Feet were more arched suggesting she walked rather than climbed trees

  • Leg structure showed she walked upright more efficiently than Ardi

c. 1.6 million years old fossil hominids found by Leaky

• Richard Leaky and his team found many fossils from different Australopithecus and Homo species. These were found in Kenya in 1984 after the scientist organised an expedition. During this they found Turkana Boy, a 1.6 million years old fossil with features more similar to humans than Lucy:

  • Brain size was larger than Lucy’s and similar to humans

  • Arm and leg sizes were more human-like

  • Legs and feet were more adapted to walking upright

V. Human Evolution and Stone Tools

• Human evolution can also be proved by looking at stone tools. This is because the tools they used slowly became more and more complex proving that the human brain developed and grew in size:

VI. Pentadactyl Limbs

• Pentadactyl limbs are limbs with 5 digits. These can also provide evidence for evolution as pentadactyl limbs are found in different species e.g. mammals, amphibians and reptiles. This suggests that these species have come from a common ancestor.

VII. Evolutionary Trees

1. Evolutionary trees can be used to show evolutionary relationships between different types of organisms.

• The two trees below can be used to map relationships between organisms.

2. In the second graph, all of the organisms have the same common ancestor.

• Each branch represents speciation. As all of the organisms come from the same first branch, they show that they are all from the same ancestor.

3. The more and more the organisms branch from one another, the more different they become.

• Therefore, the Aquifex and Thermotoga are very similar to one another, however the Aquifex and the Diplomonads, although are from the same ancestor, are very different from one another.

Unit 4: Fossil Formation

I. Fossils

• Fossils result from the preservation of dead organisms over millions of years.

• Fossil formation involves the gradual deposition of sediment or minerals over dead organisms, eventually hardening into rock.

• The fossil record comprises all discovered fossils, aiding scientists in understanding evolution and changes in life over time.

• Extinction, the permanent loss of a species, is studied through fossil analysis and DNA research.

• Prevention of extinction involves habitat preservation, pollution reduction, and regulation of harmful human activities.

• Studying fossils and extinction informs our understanding of Earth's history, species evolution, and human impact on the environment.

1. Fossil Formation

• Certain parts of organisms, like shells and bones, resist decay and can turn into rock through weathering.

2. Conditions for Decay

• Decay requires specific environmental conditions such as temperature, oxygen content, and water. Preservation can occur in environments like peat, ice, tar, and amber where organisms are isolated from decay-promoting factors.

Unit 5: Development and Understanding of Evolution

I. Evidence for Evolution

• Darwin's Theory of Evolution by Natural Selection is widely accepted due to substantial supporting evidence. Genetic inheritance, with traits passed down through generations, exemplifies natural selection, favoring characteristics that confer survival advantages.

II. Resistant Bacteria

• Antibiotic resistance illustrates evolutionary principles.

1. Bacterial Reproduction

• Bacteria exhibit rapid reproduction rates, facilitating swift evolution in response to environmental pressures.

2. Survival of Antibiotic-Resistant Bacteria

• Bacteria resistant to antibiotics have a survival advantage, leading to increased reproduction and proliferation of resistant strains.

3. Spread of Antibiotic-Resistant Strains

• Resistant bacteria propagate rapidly due to prolonged survival in the absence of effective treatment.

• MRSA (Methicillin-Resistant Staphylococcus aureus) serves as an example of antibiotic-resistant bacteria.

• Measures to mitigate antibiotic resistance include judicious prescription, completing antibiotic courses, and reducing agricultural antibiotic use.

• Developing new antibiotics is challenging and costly, with limited financial incentives for pharmaceutical companies. Additionally, research efforts may be outpaced by the emergence of new resistant strains.

Unit 6: Theory of Speciation

I. Definition

• Natural selection can lead to formation of a new species if there is a split in the population.

• For example, geographical isolation could separate two populations of monkeys over two islands.

• A mutation in one monkey (grey) can help improve ability to climb trees and reach food

• This mutation spreads via natural selection to the other monkeys on the same island. There is a reproductive barrier (the river) between both populations, so the mutation doesn’t spread to the other monkeys.

• Over time, the two populations become so different that they can no longer breed together – two different species are formed.

II. Speciation

• Darwin was in competition with another scientist. This was Alfred Richard Wallace. He independently published his own theories regarding natural selection and evolution. However, he is most famed for his ideas on speciation.

1. Wallace prompted Darwin.

• Wallace proposed a theory of natural selection at the same time as Darwin. This led to Darwin rising to the competition and publishing his own paper, On the Origin of Species the next year.

2. Wallace also worked on speciation.

• Wallace spent a lot of time looking into speciation, however we have built on these ideas over time to form a concrete theory of speciation.

III. Impact of the Theories on Biology

• The theories of evolution and speciation have influenced modern biology significantly:

1. Organism Classification

• Understanding evolutionary relationships allows for the systematic classification of organisms based on their evolutionary history.

2. Conservation Efforts

• Appreciation of genetic variation's importance in adaptation informs conservation strategies. Conservation projects, such as seed banks, preserve genetic diversity to safeguard species and their unique traits.

Unit 7: Theory of Evolution: Darwin and Lamarck

I. Charles Darwin

• Theories of evolution emerged in the 18th century, challenging the prevailing creationist views. Charles Darwin's theory, developed after extensive observations on the Galapagos Islands, is foundational in modern evolutionary biology.

II. Natural Selection

• Natural selection, a key concept in Darwin's theory, operates as follows:

1. Variation in Characteristics

• Individuals within a species exhibit variation in certain traits, such as neck length in giraffes.

2. Survival of the Fittest

• Organisms with traits best suited to their environment are more likely to survive and reproduce successfully. For instance, stronger lions have a higher chance of survival.

3. Hereditary Transmission of Traits

• Advantageous traits are passed down to offspring, enhancing their survival and reproductive success over generations.

• All of these changes take a very long period of time. Changes are only seen after many many generations.

• Darwin received a frosty reception to his critical work ‘On the Origin of Species.’ This was released in 1859. He upset many creationists, who believed that the theory challenged their notion that God created all of the plants and animals that raised on Earth.

4. Darwin's Challenges

• Darwin faced criticism and challenges, particularly from creationists, upon the release of his seminal work "On the Origin of Species" in 1859. Factors like limited understanding of genetics and lack of concrete evidence hindered widespread acceptance of his theory during his lifetime.

III. Lamarck

• Jean-Baptiste Lamarck proposed an alternative theory of evolution, emphasizing the inheritance of acquired characteristics.

1. Inheritance of Acquired Characteristics

• Lamarck's theory posited that traits acquired during an organism's lifetime could be passed down to offspring. For instance, if parents improve cardiovascular fitness through exercise, their offspring inherit this trait.

• Both Darwin and Lamarck contributed to the understanding of evolution, with Darwin's natural selection theory gaining more scientific support due to its alignment with later discoveries in genetics and empirical evidence.

Unit 8: Cloning

I. Variation in Biology

• Variation refers to differences among individuals within the same species, encompassing physical characteristics and genetic diversity.

II. Cloning

• Cloning is the process of creating identical copies of an organism or cells, with applications in reproductive, therapeutic, and gene cloning.

1. Benefits

• Cloning facilitates genetic research, medical treatments, and conservation efforts by preserving endangered species.

2. Drawbacks

• Drawbacks include ethical dilemmas, genetic abnormalities, and technical limitations associated with the cloning process.

3. Impact on Genetic Variation

• Cloning can reduce genetic diversity within a species by producing genetically identical individuals

III. Importance of Genetic Variation in Biology

• Genetic variation is crucial for evolution and adaptation, allowing species to survive and thrive in changing environments.

IV. Methods of Plant Cloning

1. Tissue Culture

• Tissue culture, also known as micropropagation, involves growing genetically identical plants from parent plant parts called explants. It enables the mass production of plants with desirable traits.

• There are many steps in tissue culture:

2. Cuttings

• Cuttings involve propagating plants from parent specimens, commonly practiced by gardeners without the need for a sterile medium.

V. Methods of Animal Cloning

1. Animal Tissue Culture

• Similar to plant tissue culture, animal tissue culture involves extracting tissue samples, culturing and growing cells in a suitable medium for research purposes.

2. Embryo Transplantation

• Embryo transplantation, facilitating the production of genetically identical offspring, is achieved by transferring embryos to host mothers.

• The steps of embryo transplantation:

a. Fertilisation

• Sperm is taken from one animal, an egg is taken from another.

b. Artificial Insemination

• An animal is then artificially inseminated.

c. Development of Embryos

• The zygotes are allowed to develop into embryos.

d. Removal of Embryos

• Embryos are then removed from the uterus of the inseminated animal.

e. Splitting of Embryos

• These embryos are split apart to form smaller cells. This process must take place before specialisation (when cells develop into different types of cells).

f. Transplant into Host Mothers

• You then transplant all of these embryos into host mothers. These embryos will all be genetically identical to one another and so will be clones.

3. Adult Cell Cloning

• Adult cell cloning, exemplified by Dolly the Sheep, involves replacing an egg cell nucleus with that of an adult cell, leading to the birth of a genetically identical organism. The process for adult cell cloning to produce Dolly is shown below:

a. Advantages

1. Produces animals with desired characteristics

   • Cloning can produce animals that are transgenic and primed to produce required proteins for the body. As clones are produced, they will have the exact genetic information as the parent cell, so the required characteristics can easily be chosen. Hence, they can be used to produce human proteins. For example, cows and sheep can produce milk containing useful human proteins, chickens can produce proteins in their egg whites and antibodies for illnesses like arthritis can also be produced through this method.

2. Helps prevent extinction

   • Another lesser known positive is the fact that it can be used to save animals from extinction. Endangered species can be cloned, in order to increase the population and then can breed to continue growing animals.

b. Disadvantages

1. Difficult process

   • Adult cell cloning is a difficult process and requires lots of intense effort.

2. Reduction in genetic variation

   • As genetically identical organisms are produced, there is an increased risk of reducing the genetic variation. This will reduce the size of the gene pool and lead to an increase in the incidence of genetic diseases.

3. Ethical issues

   • There are ethical queries. Are humans playing God by cloning? Will the cloning of animals finally transition into the cloning of humans?

Unit 9: Genetic Engineering

I. Understanding

• Genetic engineering, also known as genetic modification, involves introducing a gene from one organism into the genome of another organism to introduce desirable characteristics. It encompasses removing, changing, or inserting individual genes. While the practice is debated, many see it as a vital tool for scientific progress.

II. The Use of Bacteria

• Bacteria are instrumental in genetic engineering due to their rapid reproduction rate, ability to synthesize complex molecules like insulin, and minimal ethical concerns over their manipulation. Their genetic code is shared with all other organisms, enabling them to produce proteins from genes of different origins. Additionally, bacteria possess plasmids that are easy to modify and transfer.

III. Mechanism of Genetic Engineering

1. Select a desired phenotype

• Identify the desired characteristic or phenotype needed, such as insulin production.

2. Find the gene which causes this phenotype

• Locate the gene responsible for the desired trait, such as the insulin gene in humans.

3. Insert the gene into the recipient

• Transfer the desired gene from the donor organism to the recipient organism, often using a vector.

4. Culture the recipient

• Enable the genetically modified organism to reproduce, as in the case of cultivating insulin-producing bacteria in a fermenter.

IV. Genetic Engineering in Plants

• Genetic engineering can yield genetically modified (GM) crops with improved traits.

1. Improve crops

• Enhance crop characteristics such as disease or pest resistance, leading to better yields.

2. Aid humanitarian situations

• Address nutritional deficiencies by engineering crops like Golden Rice, enriched with beta-carotene to combat Vitamin A deficiencies.

V. Genetic Engineering in Animals

1. Produce insulin

• Genetically modify bacteria to produce insulin, offering a more efficient alternative to animal-derived insulin for treating diabetes.

2. Drive medical research

• Explore avenues for treating various medical conditions through genetic engineering, such as HIV, sickle cell anemia, Huntington's, and cystic fibrosis.

VII. Negatives of Genetic Engineering

1. Health risks

• Genetically modified foods may pose health risks due to potential allergens or toxins.

2. Ethical hazards

• Some question the ethical implications of creating genetically modified organisms.

3. Unknowns

• Concerns exist about unforeseen ecological impacts and the potential spread of modified genes.

4. Costs

• Genetic engineering processes could increase production costs, affecting affordability.

VIII. Using Enzymes to Isolate Genes

• Enzymes play a crucial role in isolating genes for genetic engineering purposes, involving steps like restriction endonuclease cleavage, plasmid vector insertion, and bacterial cell transformation.

  • This means that the bacteria have genes that were transferred into them from a different species:

1. The required gene is isolated by restriction endonuclease and produces ‘sticky ends’

• Restriction endonuclease enzymes act as scissors, cutting the genome of the human cell and removing the insulin gene. The enzymes target specific sequences of DNA and cut the DNA here. This leaves the isolated insulin gene with ‘stick ends’ – ends with unpaired bases.

2. The required gene is placed in a vector

• This can either be a virus or a bacterial plasmid. In this case, we would insert the insulin gene into a plasmid vector. The plasmid is cut open using the same restriction enzymes used to isolate the insulin gene. This creates complementary ‘sticky ends’ in the plasmid. Ligase enzymes are used to stick the insulin gene and plasmid together correctly forming a recombinant plasmid

3. The vector is then introduced into the organism

• In this case, the plasmids (with the insulin gene inserted) are transferred into a bacterial cell. This cell replicates and produces millions of bacteria that contain the insulin gene so are able to produce insulin. This insulin can be obtained and used to treat those with diabetes.

• Sometimes the vector might not be transferred into the bacterium correctly. Hence, you can identify and select those cells that have successfully been modified. You can do this using antibiotic resistant markers. A gene that codes for antibiotic resistant is inserted into the plasmid at the same time as the desired gene e.g. the insulin gene. The bacteria are cultured on a plate covered with antibiotics. The cells that grow and survive will be the ones with the antibiotic resistant gene and the insulin gene.

• Remember both sets of enzymes (restriction and ligase enzymes) are specific to certain base sequences.

• Genes must be transferred into an organism early in development. This will allow them to spend time properly growing and gaining the characteristics that were selected.

Unit 10: Selective Breeding

• Selective breeding involves choosing plants and animals with the best traits (e.g. most food producing) and breeding them more. It is also known as artificial selection as you artificially select the organisms that will breed to increase the frequency of the desired characteristic in the population.

• In this way, we are breeding for particular genetic characteristics. These characteristics can help the organism in many ways. For example, we can breed plants which are resistant to cold weather to improve production by crops in the winter.

• Humans have been doing this for thousands of year. Farmers often find wild crops or wild animals with good traits, and then breed them to produce lots of their own plants and animals with the desired characteristics.

I. Artificial vs. Natural Selection

II. Selective Breeding in Plants

• All sorts of crops are selectively bred. This includes corn, peaches and bananas.

• They are bred selectively for many beneficial characteristics, including:

  • Large fruits

  • Resistance against diseas

  • Increased crop yield

  • Greater aesthetic beauty, such as larger flowers or more unusual flowers

III. Selective Breeding in Animals

• Animals are bred selectively to increase the changes of certain characteristics. These include:

  • Increased meat yield

  • Increased milk yield

  • Large eggs from chickens

  • Desirable characteristics in domestic dogs, such as a gentle nature

IV. Mechanism of Selective Breeding

1. Choose parents with the desired characteristics

• If you are trying to breed cows with a high yield of milk, choose a cow that has a high milk yield and a bull, who’s mother had a high milk yield. They must be from a mixed population.

2. Breed them together

• Breed the selected parents together. They will both have the desired genes and hence the offspring will also gain the desired genes.

3. Breed the offspring with the desired characteristics

• Not all of the offspring will have the characteristics that are selected for, therefore you only chose the desired offspring. Then breed these together.

4. Continue this process over generations

• Like natural selection, selective breeding occurs over many generations. The process is repeated again and again, and different factors can be selected for.

V. Example of Selective Breeding

1. Harry the Farmer

• For example, Harry the Farmer has a crop of plants. His crop produce keeps suffering because of pests, which eat and ruin his crops. Out of his 5 crop fields, only the crops in field 4 survived the pests.

• Therefore Harry picks out crops from field 4, and breeds these together. The offspring will have the genes to help them survive the pest attack.

• The next generation of crops will have more resistant crops because they will have the genes from the crops in Field 4 of Generation A.

VI. Positives of Selective Breeding

1. Economical benefit

• If a farmer can grow the crops with the largest fruits and the animals with the greatest yield of meat, they will get the most money. This aids the economy as their products will be of a greater quality and thus the consumer will also be happier.

2. Domesticating animals

• You can select for more docile household pets or animals that are safer to farm with.

3. Prevent disease

• You can prevent spread of disease amongst crops by using selective breeding to develop crops resistant to disease spread by pests.

VII. Negatives of Selective Breeding

• However, selective breeding can carry several dangers. The negatives are often related to inbreeding. If you breed lots of organisms of the same family, there can be a build up of recessive alleles, which increases the risk of disease:

1. Selecting for rare diseases

• Some of the more selected for organisms have unexpected disadvantages. Through selective breeding, these disadvantages may accidentally be selected for. This is dangerous. Examples include how breeding Boxers has lead to breathing difficulties for the animals.

2. Reduced genetic variation

• By selecting for specific alleles, the genetic variation in a population decreases. This can reduce defences of the animals and plants against disease and insect attacks. This can be catastrophic for the species selected for.

3. Ethical Issues

• If organisms are purposefully bred with negative, harmful characteristics for research or other reasons, it raises ethical issues. For example, some dogs that are inbred have certain defects causing them problems.