Biology Module 6

A permanent change in the nucleotide sequences of DNA in an organism.

Mutations can occur spontaneously or they can be induced by mutagens

Any agent capable of altering the genetic constitution of a cell by chabging the structure of DNA. Mutagens can be physical, chemical or biological

- Physical Mutagens (electromagnetic radiation sources)
- Chemical Mutagens
- Naturally Occuring Mutagens (Biological/non-biological)

There are a number of types of radiation that can cause damage to an organism's DNA. Radiation that can penetrate a cell and cause damage to DNA is called ionising radiation.
Eg; UV light, Gamma rays (nuclear radiation), X-rays

Chemicals that cause genetic mutations.

Chemicals may be ingested, inhaled or absorbed through the skin. These chemicals often have a similar structure to the bases in DNA and so may be
1) Incorporated into the DNA during replication instead of correct base pair
2) Inserted in the DNA sequence, breaking bonds and creating gaps = No replication
EG: Tobacco smoke can cause cancerous growth

Naturally occurring mutagens can be divided into biological and non-biological mutagens.
Biological Mutagens include; Microbes, plants and animals
Non Biological Mutagens include: Metals like mercury and lead poisoning

Point Mutation and Chromosomal mutations

A mutation where a single base of a DNA sequences is changed (substituted), inserted or deleted (Frameshift)

A base substitution occurs when one nucleotide base is replaced with another e.g. A is replaced by C. This may result in a different amino acid being inserted into the polypeptide chain. As only one amino acid is changed, the protein formed may still be semi-functional.
- Eg: Sickle cell Anemia

insertions or deletions of base pairs that shifts the entire reading frame and may lead to a whole sequence of incorrect amino acids and the protein produced will be non-functional.

- Substitution Nonsense mutations (Nonsense = STOP)
- Substitution Missense mutations ('Miss' = changed)
- Silent mutations
- Neutral mutations

Substitution Nonsense mutations - a change from an amino acid to a stop codon. This has a severe effect as it cuts the protein short.

Substitution Missense mutations - a change to one amino acid as a base pair is substituted. The protein is less functional than the original.

Silent mutations - a change in the DNA sequence that does not result in a changed amino acid. This can happen when the base that is substituted still codes for the same amino acid.

Neutral mutations - a change in the amino acid, but not the function of the protein

A change in the number or structure of chromosomes

Deletion
Duplication
Inversion
Translocation

Occurs when a section of a chromosome is removed and not replaced, reducing the number of genes in the chromosome. This may occur due to exposure to heat, viruses or radiation.

Occurs when a section of the DNA is duplicated and inserted, increasing the number of genes on the chromosome. An example of a chromosomal duplication disorder is Fragile X syndrome.

Occurs when a section of DNA is removed, turned around 180 degrees and then reinserted into the chromosome so that the bases are in the reverse order. An example of a chromosomal inversion disorder is Haemophilia A.

Occurs when a section of DNA is moved from one chromosome to a non-homologous chromosome. This may lead to gene fusion or joining of two separate genes.

A somatic mutation is one which occurs in a somatic cell (non-reproductive cells). These mutations can never be passed on to offspring whereas a germ-line mutation occurs in the reproductive cells (sperm and ova) and these mutations can be passed on to offspring and inherited.

Somatic Mutations are not inhertiable. They may cause a cancer, for example skin cancer as a result of prolonged exposure to UV rays.

Germ-line Mutations are inheritable and thus are the source of variation in a population and if the mutation is advantageous to the species it can become the predominant characteristic or trait through the process of natural selection.

DNA has coding and noncoding regions.
- Coding regions are responsible for making proteins and are often called genes. This DNA is transcribed and translated into proteins
- Non-coding regions are those pieces of DNA between the coding regions that do not get translated into mRNA and therefore do not code for proteins.

Coding DNA can transcribe, translate, and produce proteins with structural, functional, and regulatory importance in cells.

Directly affects the sequence and type of amino acids in a protein and therefore its function, which may lead to a phenotypic change

Mutations in coding DNA regions can affect proteins involved in DNA repair, leading to increased chances and rates of mutations arising from replication errors.

Structural DNA: maintains the structure of chromosomes in DNA. EG: Centromeres and telomeres (end of chromosome)

Functional RNA: RNA which is not mRNA. EG: tRNA and rRNA

Introns: regions of RNA that are spliced out before translation

Non-coding DNA sections have regulatory sequences that "switch on" or "switch off" genes. Non-coding DNA codes for rRNA and small nuclear RNA, both of which are important for the regulation of gene expression.

rRNA (ribsomal RNA) = regulates translation of DNA
Small nuclear RNA determines which introns are spliced out of DNA (gene splicing)

Considering Non-coding DNA codes for rRNA and small nuclear RNA, both of which are important for the regulation of gene expression, a mutation in this region can affect gene expression potentially causing a protein to be produced in the wrong place or at the wrong time.

In sexual reproduction the DNA from each parent is shuffled, and the resulting offspring contains a new combination of genetic information, half from each parent, thus increased gene recombination = Increased variation.

In species that reproduce asexually, offspring inherit all the genetic information from their one parent. As a result there is much less genetic variation in the population. due to the offspring inheriting identical genetic information.

Processes such as crossing over, independant assortment and random segregation ensure genetic recombination and variation within the offspring. EG: The independent assortment of homologous chromosomes at the equator during meiosis results in new combinations of phenotypes in the offspring as they divide into daughter cells, which increases variation in the population.

Mutations can occur during DNA replication (point mutations) or when the chromosomes are sorted into daughter cells (chromosomal mutations), generating altered or new alleles (version of a gene) in which will alter the genotype/phenotype of an organism.

Eg: Crossing over errors such as a chromosomal inversion before it is reinserted into the homologous chromosome.

Mutations introduce genetic variation into populations by creating new alleles or altering existing ones. This variation is the raw material for evolutionary change and can lead to adaptive traits, allowing populations to better adapt to changing environments and improving their biological fitness. However, some mutations can reduce fitness and lead to the onset of diease and disorders within a species/organism.

The movement of alleles from one population to another, leading to the exchange of genetic material

Gene flow can increase genetic diversity within populations, reducing the effects of genetic drift and inbreeding. It can also introduce adaptive alleles or increase the frequency of advantageous traits. However, excessive gene flow can homogenize populations increasing genetic similarity between populations

An unpredictable change in allele frequencies caused by chance events.

- The Bottleneck effect
- The Founders effect

Genetic drift can reduce genetic diversity within populations, increasing the risk of an inbreeding depression and reducing the population's ability to adapt to environmental changes. However, genetic drift may also promote the rate of evolutionary change and speciation within a population due to natural selection.

Occurs when a large population is reduced in size ( e.g. by a natural disaster/ environmental damage) and the gene pool of the surviving population is much smaller than the original gene pool.

When a few individuals become isolated from a larger population and form a new population whose gene pool composition does not reflect the original population.

To make ethical decisions regarding the use of technological advances, scientists use reason and evidence rather than emotion to weigh up the benefits versus the costs of using a technology against those of not using the technology.
Costs and benefits may consider:
- medical and health benefits
- financial and social justice issues (including equity in access to technologies)
- animal and human rights
- effects on the environment

Social implications:
- GMO food safety and security
- Environmental damage of GMO crops (affecting natural pop)
- Improved quality of life (medical, agricultural and industrial)
- Medical advancements (prevention - vaccines or treatment - golden rice, human insulin)

Biotechnology is constantly changing with improvements to the complexity and precision of technologies all the time. As we make new discoveries, we can predict the future impact on individuals, society and the environment.
- CRISPR technology to create transgenic species and treat diseases such as sickle cell anemia.

- The creation of GMO foods to; Treat/prevent disease such as Golden rice for Vitamin A deficiencies, Increase yields for farmers, translating to imrpoved quality of life.
- Environmental sustainability. EG: GMO plants in which are disease resistant, reducing the need for chemical use
- The creation of personalised medicine and vaccines
- Gene therapy for disease

Genetic Technologies include cloning, selective breeding, artificial pollination, artificial insemination, CrispR, recombinant DNA, IVF etc

Genetic technologies allow scientists to modify genes, transfer genes from one organism to another and manipulate the expression of genes. Genetic technologies have been used for decades and are comminly deployed for agriuclutral, medicinal or research purposes. Current technologies include cloning and genetic engineering

Allows for the production of genetically desirable characteristics and/or traits in livestock and plants. This includes:
- Nitrogen fixing plants (Environmental sustainability (EV))
- Disease resistant plants (EV - less chemical application)
- Animals predisposed to putting on greater muscle mass (increased yieldsevenues)

- Cloning techniques are employed in therapeutic cloning to generate tissues or organs for transplantation,
- The development of gene therapies to treat genetic disorders (CRISPR)
- The production of recombinant proteins, such as insulin and growth hormones, for therapeutic use.

Assists in the study and understanding of the genetic basis of disease and developmental processes. Supports advanced research in genetics, molecular biology, biotechnology and disease

- Selective breeding
- Artififical Insemination
- In-Vitro fertilisation (IVF)
- Artificial polination

Ai: The process by which sperm is taken from a genetically superior bull via an artficial vagina. Sperm is then frozen, placed in a straw and inserted into the cervix on ovulation.

Ap: Involves the removal of the stamen (male parts) of a flower and dusting pollen onto the stigma of the same plant (self-pollination) or a different plant (cross-pollination).

Ai: Allows for greater control in the production of an offspring, quicker multiplication of desireable traits in a herd and a highly successful/cheaper means of producing a superior animal

Ap: Allows greater control of which plants breed, increases the chance of pollination and the creation of new varieties and hybrids. Artificial pollination can therefore increase variation in a species by creating new combinations of alleles.

Reproductive cloning (whole organism) - the production of a genetically identical organism, using a somatic cell from a mature individual. EG: Dolly the sheep

Gene cloning - the production of identical copies of one gene. These copies may be used for genetic engineering and research.

Somatic cell nuclear transfer (SCNT) - transferring a somatic cell (Non-reproductive) nucleus into an enucleated (egg has been removed) egg cell to create an embryo that can develop into a clone.

Artificial Embryo Twinning - artificially splitting an early embryo into multiple parts, each developing into a genetically identical organism

Plant Propogation - uses vegetative parts of plants to produce new plants, ensuring genetic uniformity and enabling mass production

1. The gene is cut from the source organism using restriction enzymes produced by bacteria.
2. The gene is pasted into a vector DNA or plasmid using ligase enzymes to join fragments of DNA (ligation).
3. The plasmid containing the gene is introduced to a host cell (transformation).
4. The host cell then makes copies of the vector DNA when it makes copies of its own DNA (DNA Replication).

Restriction Enzymes are enzymes that cut DNA at specific sequences, allowing for precise manipulation and recombination of DNA fragments

A Technique used to exponentially amplify large numbers of a specific sequence of DNA. Performed through a PCR machine in which uses variations in temperatures to control the replication process.

Recombinant DNA technology involves inserting a gene from one species into the genome of another.
- Can be used to create transgenics species

Transgenic species can be created using recombinant DNA technologies as a gene is taken from one species and inserted into the DNA code of another species.

1. The required gene is isolated from a cell.

2. A plasmid (piece of circular DNA) is removed from bacteria.

3. Two pieces of DNA are cut using the same restriction enzyme.

4. These strands have matching "sticky ends" (sections of single-stranded DNA with exposed bases at the end of the double-stranded molecule).

5. The bacterial plasmid is cut at 2 points with the same restriction enzymes.

6. As the sticky ends of the donor organism and the plasmid come together, they join via base pairing.

7. DNA fragments are joined by the enzyme ligase.

8. The plasmid is inserted back into the bacterial cells where multiple copies of the gene are produced. Once this has happened, the gene can be inserted into an egg cell of another species and, after fertilisation, it will become part of the newly-formed organism's DNA.

1. Microinjection of DNA into the nucleus of an egg.
2. Biolistics (or "gene guns") to mechanically deliver DNA on microscopic particles into target cells and tissues.
3. Electroporation to increase the membrane permeability by applying an electric current.
4. Transduction by a vector e.g. a virus, liposome or bacterial plasmid to carry DNA into the cells.

Agriculture:
- Bt cotton: contains a gene from the bacteria Bacillus thuringiensis (Bt) which makes the plant resistant to pests.
- Enviropigs receive genes from bacteria and mice that enable them to produce an enzyme to break down phosphorus which is currently a problem with pig faeces high in phosphorus causing environmental damage.

Medicine:
- Creating products such as human insulin or blood clotting factors

- May be able to produce crops that are better suited to the environmental conditions e.g. drought resistant, etc.
- Natural pest resistance of modified crops, so fewer chemicals will be used.
- Increased yield of crops or livestock.
- More nutritious foods (Biofortification) e.g. rice with more protein, iron or vitamins.e.g Golden Rice
- Animals that grow larger and faster e.g. "Super salmon"

- Produce products for medical treatments e.g. Humulin (human insulin) to treat people with diabetes.
- Artificially clone antibody-producing cells that target specific antigens e.g. in cancer treatment to target cancer cells. This can be used to; activate the immune system, block the immune system, stop cell division of cancer cells and assist in the delivery of other treatments

- GM plants producing environmentally friendly chemicals to replace non-renewable products such as fuel, plastics, paint, etc.
- Starch from potato plants isbeing explored as an alternative for paper and textile production
- Produce enzymes for food production more quickly and in larger quantities than by natural means.
- Production of GM plants and bacteria to absorb heavy metals (e.g. mercury) from contaminated sites to help restore mine sites and heavily polluted areas.

The use of biotechnology may (has the potential to) increase or decrease the genetic diversity of a species.
For example:
- Selective breeding can initially increase genetic diversity by introducing new alleles to a population. However, in the long term, genetic diversity tends to decrease as selected genes are constantly replacing other variations.
- Cloning will reduce genetic diversity as individuals with identical genetic codes are produced.
- Transgenics will initially increase diversity by introducing a new gene to the genetic code. However, transgenic organisms are often cloned to easily reproduce offspring with the gene which could lead to decreased diversity.

Cloning = decrease
Selective Breeding = Decrease
Artificial Polination - Decrease
Artificial Insemination = Decrease
Recombinant DNA = Initial increase but potential decrease

Initially it may increase biodiversity by introducing new gene combinations in the population or new genes in the individual. However, if these organisms are then reproduced and bred due to the desirable characteristics, biodiversity may be reduced.

Another concern is the potential for genetically modified organisms to breed with wild varieties of plants and animals with the potential for this to impact biodiversity. If the genes of the GM organism are advantageous, the frequency of the allele will increase but this may lead to them outcompeting the natural species, leading to its extinction.

The social context is the physical and social setting in which we live. The biotechnological advances that are developed are determined by the needs of that society

DNA fingerprinting can be used for paternity testing and forensic analysis of crime scenes. The information gained from this enables a high degree of accuracy in matching samples and problem solving

- The process is expensive and time consuming
- Access to the process may not be equitable
- Discrimination and privacy issues in relation to genetic information obtained as well as inappropriate use of the technology

The economic context relates to GMO's and the need for producers to make profit on their products while allowing consumers to purchase at an affordable price

The main issues include:
- Biotechnology companies rights and monopoly over their technologies
- GM crops may offer improved yield, so their will be increased financial return to farmers and lower prices to consumers

The cultural context refers so the values, religious/moral beliefs, and education of a group and how these factors may influence their opinions on the use of biotechnologies.

EG: 'Mungo Man' DNA testing was approved by the traditional custodians of the land and accepted as it had the potential to prove their values in which relate to how the aboriginal population was and is the first human population to live in Australia