Fossils

Define fossil

Remains or traces of organisms, generally formed from hard/solid body parts like bones and teeth, that have been preserved.

List 5 different forms of fossils

• Bones

• Shells

• Footprints

• Burrows

• Impressions of part or all of an organism.

Distinguish between fossils and artefacts.

An artefact is an object that has been deliberately made by humans. E.g. stone tools, beads, carvings, charcoal from fires/hearths and cave paintings. Where as fossils are the preserved remains or traces of organisms that once lived.

Outline the conditions suitable for fossil formation.

• Fossilisation most commonly occurs with solid body parts like bones and teeth; many organisms without hard structures are not preserved.

• Rapid burial is crucial at the time of death, meaning the remains are quickly covered by sediments.

• Specific sediment features are required, such as low pH (acidic) and anaerobic conditions (lack of oxygen) or alkaline soils, to inhibit decay.

• The organisms must be protected from decay by microorganisms.

• The body/remains need to be undisturbed by scavengers or geological processes for a long time to allow fossilisation to take place.

Explain that the fossil record is incomplete and cannot represent the entire biodiversity of a time or a location due to many factors e.g. the factors that affect fossil formation, the persistence of fossils and the accessibility to fossilised remains.

• Limited Preservation of Soft Body Parts: Most fossils form from solid parts like bones and teeth; many organisms lack hard structures and are therefore not preserved.

• Specific Conditions for Fossilization: Requires rapid burial, specific sediment features (e.g., low pH, anaerobic conditions), and protection from decay, which are uncommon.

• Decay and Scavenging: Organisms often decayed by microorganisms or are scavenged before fossilization can occur.

• Disturbance and Destruction: Fossils need to be left undisturbed for long periods. They can be destroyed by geological processes (volcanic eruption, earthquakes, faulting, folding), weathering, erosion, or human/animal activity.

• Accessibility and Discovery: Many fossils are buried too deep to be found or are not recognized as fossils. Scientists may also not be looking in the right places.

• Biodiversity Representation: Due to these factors, many organisms are simply not preserved, and dating can sometimes be impossible, limiting the fossil record's ability to represent the full biodiversity of a time or location.

Define absolute dating

Give an actual age in years for a fossil or artefact e.g. 1.5 million years BP (before present)

Define relative dating

Determines the relative age of fossils or artefacts by comparing them to others, typically based on their position in rock strata. It does not provide actual numerical dates.

Types of relative dating

Stratigraphy and index fossils

Describe what is studied in stratigraphy.

Involves the study of rock strata/layers. Scientists study these layers to match similar strata to other strata already dated, or to infer relative age based on the position of layers.

Explain the principle of Superposition

It assumes that rock layers are deposited over time, meaning further down a layer the older a layer is and newer layers are laid on top. Fossils found in lower layers are generally older.

Limitations of superposition

Earth movements such as folding or faulting can alter strata levels, causing older layers to appear above younger ones. Erosion or animal/human burial can also introduce materials into lower strata, misleading relative dating.

Define correlation of rock strata

The correlation of rock strata is a method used in stratigraphy to determine the relative age of rock layers and the fossils they contain, particularly when absolute dating is not possible or insufficient.

Explain how the correlation of rock strata is used to determine the relative age of strata.

Rock strata from one location are matched with another location based on similar characteristics. This process allows for the determination of relative age by assuming that artefacts or fossils in matching strata are the same age across different sites. The presence of index fossils can also aid in this correlation.

Explain what an index fossil is and how they are used in relative dating.

• Index fossils are fossils that are widely found across different geographical locations but only existed for a limited, known time span on Earth. They are also recognizable and found in large numbers.

• They have a known date/age range. If an index fossil is found alongside other fossils in a stratum, the age of those other fossils can be correlated based on the known age range of the index fossil. For example, Homo sapiens could be an excellent example due to being widespread across all continents.

Explain the significance of fossilised pollen grains in dating.

Preservation and Nature of Pollen:

• Pollen is an incredibly inert substance that can stay intact for thousands of years, particularly when preserved in bodies of water, peat, or lake sediment.

• While often too small to be seen with the human eye, these minuscule microfossils can be identified using a scanning electron microscope (SEM).

• Pollen from different plants comes in a variety of distinct shapes and sizes, which aids in their identification.

 

Dating through Pollen Zones and Correlation:

• Pollen dating is primarily done by comparing the pollen zones in different rock layers or strata.

• This involves comparing older, deeper layers to newer ones on top.

• A "pollen zone" refers to a particular time frame where specific species of plants release more pollen into the air than others.

• By identifying these zones, scientists can determine the relative age of the strata.

• The presence of certain pollen types in fossil deposits helps palaeontologists determine how long ago the fossils formed.

 

Environmental and Historical Insights:

• Fossilised pollen provides valuable information beyond just dating; it helps reconstruct past ecosystems.

• It can be used to determine climate changes, evidence of deforestation, or changes in land use over hundreds of years. For instance, an increase in ragweed pollen has been associated with European settlement in North America.

• Specific locations can even be identified as the origins for many rare or uncommon pollens.

• By analysing the variety and relative abundance of microfossils, including pollen, in fossil sites, scientists can better understand Australia's past.

• For example, pollen from a relative of the Southern Beech was a dominant plant in the Miocene of Australia, indicating its prevalence during that period.

Types of absolute dating

Radiocarbon (C-14) dating and potassium-argon dating

Define isotope

 

• Isotopes are different versions of the same element.

  • They have the same number of protons (so they are the same element).

  • But they have a different number of neutrons (so their mass is different).

• Some are unstable or radioactive — they break down over time and give off radiation. This is called decay.

• Half-life is the amount of time taken for half of the radioactive substance to decay.

How are Isotopes used in absolute dating?

• Isotopes are used in absolute dating methods, specifically through radiometric (or radioisotope) dating, which provides the actual chronological age of a fossil or artefact in years.

• These methods are based on the principle that certain radioactive isotopes decay at a constant, measurable rate

Describe the potassium-argon technique of absolute dating

This technique involves measuring the radiation produced from a sample and determining the ratio of potassium-40 to argon-40 (or calcium-40) in the rock. It utilizes the half-life of potassium-40, which is approximately 1.25 – 1.3 billion years, to calculate the actual age of the rock or material.

Limitations of Potassium-Argon Dating:

• Limited Age Range: Potassium-argon dating can only date rocks older than 100,000 to 200,000 years. This is because after 100,000 years, only a very small percentage (0.0053%) of potassium-40 would have decayed to argon-40, which is near the limits of detection devices.

• Rock Type Suitability: Not all rock types are suitable for this dating method. It primarily works on igneous rocks formed from cooled volcanic lava.

• Indirect Fossil Dating: To date a fossil, there must be sufficient suitable rock of the same age as the fossil available. This usually happens when volcanic ash or lava buries bones. This means the fossil itself is not directly dated, but rather the surrounding rock layers.

• Gas Retention: This method relies on the assumption that the argon gas produced by decay remains trapped within the rock. If the rock has been heated or disturbed, argon gas can escape, leading to inaccurate dating results (this specific detail about gas escape is an external insight to the sources, but directly related to the concept of decay and measurement).

Describe C-14 (radiocarbon) dating

This method is based on the decay of carbon-14 into nitrogen. The amount of carbon-14 within an organism is fixed at the time of its death. The ratio of remaining carbon-14 to stable carbon-12 in the sample determines its age. Carbon-14 has a half-life of 5730 years. It is suitable when useable organic material is found.

Limitations of Carbon-14 dating

This technique is unsuitable for specimens older than 60,000 – 70,000 years due to the relatively short half-life of carbon-14. Variations in atmospheric carbon-14 levels over time can impact the accuracy, as they affect the initial ratio.

Describe why AMS radiocarbon dating is superior to C-14 dating

• AMS radiocarbon dating is superior to the normal method of C-14 dating primarily due to its ability to date much smaller samples.

• While the normal method of radiocarbon dating requires at least three grams of organic material, accelerator mass spectrometry (AMS) radiocarbon dating can be used to date samples as small as 100 micrograms (0.0001 grams).

• This refined technique involves breaking the sample up into atoms so that each one can be counted.

• This capability has enabled the accurate dating of materials like tiny amounts of charcoal, saliva, and blood found in cave paintings.

Limitations of AMS Radiocarbon dating

• Limited Age Range: It generally cannot be used to date samples older than about 60,000 years. After this period, the percentage of carbon-14 remaining is too small (only 0.021% after 70,000 years) to be measured accurately.

• Organic Material Requirement: The material to be dated must contain organic compounds (compounds from living things that contain carbon). This means it is only suitable for dating organic fossils of once-living organisms.

• Atmospheric C-14 Variation: The amount of carbon-14 in the atmosphere is known to vary, which means that radiocarbon dates must be treated with a degree of caution. Furthermore, industrial activities and nuclear bomb tests in the mid-20th century have also altered the atmospheric ratio of carbon-12 to carbon-14, which could complicate future carbon-14 dating.

Explain what recombinant DNA technology is / genetic engineering

This biotechnology involves locating and cutting out a specific gene of interest from one organism (e.g., a human chromosome) using restriction enzymes. This gene is then inserted into a vector, typically a plasmid, using DNA ligase, creating a recombinant plasmid. The recombinant plasmid is subsequently introduced into a host cell (e.g., a bacterium). The host cell can then propagate/replicate, and express the inserted gene to synthesize the desired protein, hormone, or vaccine in large quantities.

Describe the role of restriction enzymes in recombinant DNA technology.

Restriction enzymes (endonucleases) are crucial for cutting DNA at specific recognition sites. They are used to excise the gene of interest from the source DNA, often producing "sticky ends" (staggered cuts). The same restriction enzyme is used to cut the plasmid (vector), ensuring that the plasmid has complementary sticky ends to allow the gene of interest to be inserted.

Name 2 restriction enzymes

• Bacillus amyloliquefaciens (BamHI)

• Escherichia coli (EcoRI)

Outline the process used to make recombinant DNA, including the role of recognition sites and DNA ligase.

1. Locate the gene of interest on the source organism's DNA.

2. Cut out the gene using restriction enzymes at specific recognition sites, which produce complementary "sticky ends".

3. Isolate a plasmid (a small, circular DNA molecule) from a bacterium to serve as a vector.

4. Cut the isolated plasmid with the same restriction enzyme used for the gene of interest, creating complementary sticky ends on the plasmid.

5. Insert the gene of interest into the opened plasmid.

6. Treat the mixture with DNA ligase, an enzyme that joins the gene of interest into the plasmid backbone, forming phosphodiester bonds and creating a recombinant plasmid.

7. Introduce the recombinant plasmid into a host bacterial cell.

8. The host bacterial cells then propagate/replicate, expressing the inserted gene to synthesize the desired protein/hormone in large quantities.

Describe the differences between ‘blunt’ and ‘sticky’ ends.

Blunt Ends:

• Result when a restriction enzyme cuts the DNA straight across the double helix.

• Both ends terminate in a base pair.

• They form straight, even ends.

 

Sticky Ends:

• Result when a restriction enzyme cuts the DNA in a staggered fashion.

• This creates an overhang, which is a stretch of unpaired nucleotides.

• These exposed strands can rejoin to DNA with complementary base pairs, even if they are from a different organism. This property makes sticky ends very useful in recombinant DNA technology.

Explain what vectors (including plasmids and bacteriophages) are and where they are found, and outline why they are useful in gene technology.

• Plasmids are small, circular DNA molecules found naturally in bacteria. (The sources do not explicitly mention bacteriophages in detail as vectors.)

• They are useful in gene technology because they can act as carriers (vectors) to introduce foreign DNA (the gene of interest) into a host cell. Once the recombinant plasmid is introduced into a host bacterial cell, it can replicate independently, ensuring that the gene of interest is copied and expressed to produce large quantities of the desired protein, hormone, or vaccine.

Explain the aim of gene therapy

Gene therapy aims to treat or cure genetic abnormalities by identifying faulty genes and inserting healthy ones. This process involves adding a corrected copy of a defective gene to cells where it is needed, with the goal of helping diseased tissues and organs function properly.

Describe how gene therapy can be used to treat genetic disorders – e.g. cystic fibrosis and diabetes mellitus.

Cystic Fibrosis (CF):

• Description: Cystic fibrosis is a genetic condition caused by a recessive gene on chromosome 7. This faulty gene affects a protein that controls the movement of salt in and out of cells. This leads to thick mucus clogging organs, particularly the lungs and pancreas, resulting in repeated infections, blockages, and irreversible lung damage. The specific gene is known as the CFTR gene (cystic fibrosis trans-membrane regulator).

• Gene Therapy Approach: Trials for CF gene therapy began in the 1990s. The recombinant normal CFTR gene is inserted into a modified virus or a vesicle for delivery. These vectors are typically placed in large numbers into a nebulizer, which converts them into water droplets for delivery into the lungs during inspiration.

 

Diabetes Mellitus (Type 1):

• Description: Type 1 diabetes is a condition characterized by abnormally high blood glucose levels due to insufficient insulin production.

• Gene Therapy Approach: Gene therapy is currently being investigated as a treatment for Type 1 diabetes. While the sources confirm that gene therapy aims to treat such genetic abnormalities by inserting healthy genes, they do not provide specific details on the exact mechanism or success of gene therapy for Type 1 diabetes beyond stating it is a target for research. The goal, consistent with the general aim of gene therapy, would be to correct the underlying genetic flaw responsible for the insufficient insulin production.

Describe some difficulties associated with gene therapy.

Delivery vehicle or vector issues:

• Modified viruses or vesicles, commonly used as vectors, may not be easily taken into the target cells where the gene is needed, such as lung epithelial cells in cystic fibrosis.

• Depending on the vector used, these vehicles can sometimes cause an immune response in the patient, which can hinder the therapy's effectiveness or lead to complications.

 

Challenges with gene integration and expression:

• Delivery of the healthy gene into the cell’s chromosomes is an issue, meaning it might not integrate permanently into the host cell's genome.

• Even if the gene is successfully delivered, its mere presence does not always guarantee gene expression. The cell's machinery might not use the new genetic information to produce the necessary proteins.

• If the gene does not become inserted into the cell’s genome, its benefits will be short-lived, which means the costly therapy would need to be re-administered repeatedly.

 

Incomplete tissue coverage:

• One significant problem, particularly in conditions like cystic fibrosis, is the difficulty in delivering the normal gene to all of the affected cells (e.g., on the lung surface). This can limit the overall therapeutic impact.

 

Complexity of genetic conditions:

• Gene therapy is primarily considered a good candidate for single-gene disorders, where correcting one or a few functional genes might suffice. Conditions involving many genes and environmental factors are often poor candidates for this approach.

• For successful gene therapy, scientists need to know precisely which genes are involved in the disorder and have a DNA copy of that gene available.

• A comprehensive understanding of the biology of the disorder is crucial, including the role of the protein encoded by the gene within the cells of the affected tissue, and how mutations affect its function.

• Sometimes, simply adding a functional copy of a gene is not enough to fix the problem; in certain cases, getting rid of a defective gene or a "misbehaving" protein might be necessary, adding layers of complexity to the therapeutic strategy.

Explain the potential of cell replacement therapy in treating nervous system disorders such as Alzheimer’s and Parkinson’s diseases. (Review both diseases as they relate to the nervous system.)

Parkinson's Disease:

• Cause: Involves the damage or degeneration of nerve cells (specifically in the substantia nigra/basal ganglia region of the brain), leading to reduced dopamine levels. Dopamine is crucial for the smooth control of muscles and movement.

• Cell Replacement Therapy Potential: Aims to replace these damaged dopamine-producing neurons with healthy stem cells to restore dopamine levels and improve motor control.

 

Alzheimer's Disease:

• Cause: Characterized by the shrinkage or reduction in size of the cerebral cortex. This occurs as neurons die or are injured, and the connections between neurons break down.

• Cell Replacement Therapy Potential: Seeks to replace the damaged neurons with healthy stem cells that can form new brain cells and potentially reduce protein deposits or slow the progression of neuronal degeneration.

What is tissue engineering

Tissue engineering is a biotechnology that focuses on restoring healthy tissues or organs for patients, aiming to eliminate the need for traditional tissue or organ transplants. This field utilizes stem cells and other cellular processes to create products beneficial to humans.

Uses of tissue engineering

• Bone, skin, cartilage, and adipose (fat) tissue.

• Reconstructive surgery to repair damage from congenital defects (e.g., cleft palate), tumour removal, or traumatic injuries (e.g., burn victims).

• "Spray on skin" for burn victims, which uses skin cells sprayed onto burns to prevent the need for skin grafts and significantly reduce scarring by speeding up skin coverage.

• Potentially, entire organs can be regenerated using stem cells.

Requirements for Tissue Engineering

• An abundant supply of disease-free cells of a specific type. Early studies faced issues where cells from intended patients with genetic diseases were not successful, or not enough healthy cells were available for culture, problems which stem cell use has helped overcome.

• The creation of an extracellular scaffold for the tissue or organ to grow in a three-dimensional manner. This scaffold can be made from natural or synthetic materials and serves as a template for tissue growth.

• Scaffolds must have high pore sizes to enable cell growth and allow for the diffusion of nutrients throughout the structure.

• Scaffolds need to be biodegradable, so they can be reabsorbed by surrounding tissues without surgical removal. The rate of biodegradation must be carefully established to match the rate of tissue transformation.

• Chemicals that act as cell communicators are required to stimulate cell growth and differentiation.

How Tissue Engineering is Achieved

1. An abundant supply of disease-free cells of the specific type needed is obtained.

2. These cells are then induced to grow on a scaffold made of natural or synthetic material to produce a three-dimensional tissue.

3. Suitable stem cells are cultured and then seeded onto the scaffold.

4. The cells continue to grow and proliferate on the scaffold.

5. The cell-covered scaffold is then inserted into the patient at the site where new tissue is required.

6. As the cells continue to grow, the scaffold breaks down and is absorbed by the body.

Explain what is meant by a synthetic hormone and list some conditions/dysfunctions that are controlled or treated using these.

A synthetic hormone refers to a hormone that is artificially manufactured, rather than being produced naturally by an organism's endocrine system. These are proteins created through recombinant DNA technology.

• Diabetes mellitus

• Hypothyroidism

• Hyperthyroidism

Define genome

Complete set of genetic information of an organism.

 

Describe how DNA provides evidence for evolution (comparative genomics and mitochondrial DNA).

Comparative Genomics: Involves comparing the genome (genomic sequence), including the DNA sequence, genes, gene order, and regulatory sequences, between different species. The greater the degree of alignment (similarity) of the genome, the closer the evolutionary relationship between the species, implying a more recent common ancestor. This approach works on the principle that common features shared by organisms are often encoded in DNA that has been conserved evolutionarily.

Describe the structure and inheritance of mitochondrial DNA. Outline how mitochondrial DNA can be used to provide evidence for evolution.

• Structure and Inheritance: mtDNA is genetic material found within the mitochondria. It is typically found in small circular molecules/plasmids. A distinctive feature is that mtDNA is inherited exclusively from the mother (via the mitochondria present in the mother’s ova).

• Evidence for Evolution: Mutations occur more readily (at a higher rate) in mtDNA than in nuclear DNA. The number of mutations observed within a mtDNA molecule can be correlated with the time elapsed since divergence. The greater the diversity in mtDNA between two groups, the less closely related they are (conversely, less diversity indicates a closer relationship). This allows for the construction of phylogenetic trees to determine when divergence of species (e.g., Homo neanderthalensis from modern humans) occurred. Similarities in mtDNA can be used to directly identify genetic relatedness.

What are endogenous retroviruses

Endogenous retroviruses (ERVs) are viral sequences that have become part of an organism's DNA.

The value of ERVs in the study of evolution stems from how they become endogenous and are subsequently inherited

• A retrovirus only becomes endogenous if it inserts into a germ cell (such as an ovum or a sperm cell), meaning its genetic material will be inherited by the next generation.

• The offspring of the infected individual will then inherit a copy of this ERV in the exact same place within the same chromosome, and this copy will be passed on to all subsequent generations.

  Therefore, the presence of the same ERVs in identical locations across different species serves as compelling evidence that these species shared a common ancestor. If a retrovirus was inserted into the genome of a common ancestor, it would be inherited by all descendant species at precisely the same chromosomal location. The greater the similarity of ERVs, or the presence of the same ERVs, indicates a more recent common ancestor or less time since divergence.

Describe how comparative protein studies provide evidence for evolution.

• Comparative biochemistry (which includes protein studies) examines evolutionary relationships between species by looking at similarities and differences in their chemical makeup.

• For example, studying the similarities and differences in neurotransmitters (a type of chemical/protein) between species can help establish their relatedness. The more similar the structure or function of homologous proteins between species, the more closely related they are considered to be, suggesting a shared common ancestor.

Define ubiquitous protein and name one example.

A ubiquitous protein is a type of protein that is found in all species. These proteins perform very basic, but essential tasks that are required for life in all organisms. Example: cytochrome C.

Describe how study of ubiquitous proteins provides evidence for evolution.

• Amino Acid Sequence Comparison: Proteins, including ubiquitous ones, consist of long chains of specific amino acids linked together in a precise sequence. By analysing the type and sequence of amino acids in similar proteins from different species, the degree of similarity can be established.

• Indicator of Shared Ancestry: The more similar the amino acid sequences of a ubiquitous protein are between two species, the more recently they shared a common ancestor. Conversely, a greater difference in amino acid sequence indicates that species are more distantly related, as more time has passed since their last common ancestor.

• Conservation of Essential Functions: The fact that certain amino acid positions in ubiquitous proteins remain unchanged across vast evolutionary timescales (e.g., 37 of 104 amino acids in human cytochrome C are found at the same positions in every sequenced cytochrome C molecule) strongly suggests that these proteins descended from an ancestral molecule that existed in a primitive microbe over 2000 million years ago. This conservation highlights the fundamental importance of these proteins for life.

• Quantifying Relatedness: The degree of difference between protein sequences allows scientists to estimate the amount of evolution that has occurred since two species diverged from a common ancestor. For example, the cytochrome C of chimpanzees and gorillas is identical to that of humans, while rhesus monkeys differ by only one amino acid compared to humans. This suggests a very close evolutionary relationship.

What is bioinformatics?

Bioinformatics is an interdisciplinary field that combines computer science, statistics, mathematics, and engineering to analyse large amounts of biological and genetic data.

What is bioinformatics use to evolutionary biologists

• Enables large-scale, computerized analysis of genomic and proteomic data.

• Allows for the determination of the degree of similarity between different species' DNA or protein sequences.

• A higher degree of similarity suggests a more recent separation from a common ancestor.

• This analysis helps evolutionary biologists to construct phylogenetic trees and models of evolutionary relationships, indicating where species are placed on these trees.

• Techniques like image and signal processing extract results from raw data.

Describe what the process of annotation enables.

The process of annotation enables the identification of genes and other biological features within a DNA sequence.

Interpret phylogenetic trees to determine evolutionary relationships between groups.

• Phylogenetic trees are diagrams that represent the evolutionary relationships between organisms.

• They illustrate how recently species evolved from common ancestors:

  • Species that share a more recent common ancestor are considered more closely related.

  • Species that share a less recent (older) common ancestor are considered less closely related.

• It's important to remember that phylogenetic trees are hypotheses or possible pathways of relationships, not absolute facts.

• For example, a tree might show Australopithecus afarensis as a common ancestor to various hominin species, or indicate divergences between Homo and Paranthropus species based on shared ancestry.

Understand that developments in the fields of comparative biochemistry (including DNA and protein sequences) and bioinformatics help refine existing models and theories related to evolutionary relationships.

Refining Evolutionary Models with Biotechnology - Developments in comparative biochemistry (which includes analysing DNA and protein sequences) and the application of bioinformatics are critical in advancing and refining existing models and theories related to evolutionary relationships. These tools allow for precise comparisons of genetic and biochemical similarities, providing deeper insights into evolutionary pathways and relatedness.

List 4 techniques used in identifying genes and alleles

• PCR (polymerase chain reaction)

• Gel electrophoresis

• DNA sequencing

• Gene probes

Outline the purpose of PCR.

The Polymerase Chain Reaction (PCR) is a biotechnology application used to amplify or create many copies of specific regions of DNA. This is useful for obtaining enough DNA from a tiny sample for further analysis (e.g., from fossils, viruses/bacteria, or for genetic disease detection).

Describe the steps in PCR

1. Denaturation: The DNA sample is heated to a high temperature (e.g., 94-96°C) to separate the double-stranded DNA into two single strands by breaking the hydrogen bonds between complementary base pairs.

2. Annealing: The temperature is lowered (e.g., 50-65°C), allowing short DNA sequences called primers to bind (anneal) to their complementary sequences on the single-stranded DNA templates. TAQ polymerase is also added at this stage.

3. Extension/Elongation: The temperature is increased (e.g., 72°C), and TAQ polymerase (a heat-stable DNA polymerase) synthesizes new complementary DNA strands by adding nucleotides to the primers, extending the DNA segment. These three steps are repeated for many cycles (typically 20-40) to exponentially amplify the DNA.

Describe what is meant by the term ‘DNA profile’ (DNA fingerprint).

A DNA profile (or DNA fingerprint) refers to a unique pattern of DNA fragments that is specific to an individual. This pattern can be obtained and visualized using techniques like gel electrophoresis.

Explain how a DNA profile can be obtained using gel electrophoresis.

1. Preparation: DNA is first extracted and often amplified (e.g., by PCR). It may then be cut into fragments using restriction enzymes.

2. Loading: The DNA fragments are loaded into wells at one end of a gel (e.g., agarose gel).

3. Electrophoresis: A weak electric field is applied across the gel, with a positive terminal at one end and a negative terminal at the other. Since DNA is negatively charged, the fragments are pulled towards the positive electrode.

4. Separation: The gel acts as a sieve. Smaller DNA fragments move faster and further through the gel, while larger fragments move slower and less far due to greater resistance.

5. Visualization: This process separates the DNA fragments into a unique pattern of bands based on their size. These bands can then be visualized (e.g., using dyes or fluorescent markers) to create the DNA profile.

Describe some uses of DNA profiling.

• DNA profiling/DNA fingerprinting for individual identification.

• Comparing an individual’s DNA to a library of DNA from known individuals (e.g., in forensic science).

• Tissue typing for matching transplant organs.

Describe what is meant by DNA sequencing

DNA sequencing is a process used to determine the precise order of the nucleotides (adenine, guanine, cytosine, and thymine) in a gene of interest or a sample of DNA. The process generally involves using DNA polymerase and fluorescent dideoxynucleotides to create DNA fragments of varying lengths, which are then separated to reveal the sequence.

 

Describe the uses of DNA sequencing.

• Identifying disease-causing mutations and establishing a long-term prognosis for inherited diseases.

• Family planning.

• Paternity/maternity testing.

• Constructing phylogenetic trees and understanding evolutionary relationships by comparing DNA sequences between organisms.

• Identifying the degree of genetic variation, similarity, or diversity within populations or between species.

• Establishing molecular clocks to determine the time elapsed since organisms shared a common ancestor.

• Understanding how genes derived from common ancestors have changed over evolutionary time.

• Used in comparative genomics.

Distinguish between DNA profiling and DNA sequencing.

• DNA Profiling focuses on comparing specific, variable regions of DNA to produce a unique pattern, primarily for identification and relatedness, without necessarily determining the exact nucleotide sequence.

• DNA Sequencing involves determining the exact order of every nucleotide in a DNA segment or entire genome, providing much more detailed genetic information for understanding genes, mutations, and precise evolutionary relationships.

Outline some ethical considerations with regards to genetic information

• Autonomy/Personal Responsibility: Individuals have the right to access their personal genomic information and to be informed about its implications, along with access to appropriate support.

• Confidentiality: Genetic information is highly sensitive, and its access should be strictly controlled and limited to prevent misuse.

• Privacy: Individuals have a right to control who has access to their personal genomic information and to ensure it remains private, addressing concerns about companies or even family members having access.

• Equity: Ensures the right to equal and fair treatment for individuals based on their personal genomic information, preventing discrimination.

• Unbiased Information and Support: Individuals should receive unbiased information and advice to consider available options regarding their genetic data.

• Potential Distress/Harm: Awareness of the potential for distress or harm caused by revealing unknown genetic relationships or predispositions.

• Ownership: Questions arise regarding the ownership of genetic information – does it belong to the individual or the company/research institution that collected it?.

• Misuse by Third Parties: Concerns exist about how health providers or insurance companies might use or misuse genetic information.

• Financial Cost: The cost of genetic testing and managing newly uncovered health issues is also an ethical consideration.

Explain what a genetic probe is

A genetic probe, also referred to as a DNA probe, is a short, single-stranded DNA molecule designed to have a base sequence that is exactly complementary to a specific gene or DNA sequence of interest. These probes are artificially manufactured and are labelled with a detectable marker, such as a fluorescent marker or a radioactive isotope, which allows them to be easily identified.

list some uses of genetic probes.

• Disease Prediction and Diagnosis: They are widely used to detect gene sequences associated with various genetic disorders. Specific conditions that can be identified include:

  • Cystic fibrosis.

  • Some forms of haemophilia.

  • Muscular dystrophy.

  • Huntington's disease.

  • Thalassaemia.

  • Tay-Sachs disease.

  • More broadly, they can check if an individual carries a specific hereditary disease-causing sequence, which can inform treatment or counselling.

• DNA Profiling and Paternity Testing: While not always the sole method, genetic probes can contribute to DNA fingerprinting techniques used in forensic investigations to match DNA found at a crime scene to a suspect, and for paternity or maternity testing to establish biological parentage.

• Detection of Foreign DNA: They are employed to identify specific DNA sequences from other organisms within a sample. An example includes the detection of horse DNA in food products like beef mince.

• In Polymerase Chain Reaction (PCR): Specific fluorescent probes are utilized in advanced PCR applications, such as real-time reverse transcription PCR (rRT-PCR) tests for viruses (e.g., SARS-CoV-2, which causes COVID-19). These probes help confirm and quantify the presence of viral genetic material amplified during the PCR process.

• Gene Isolation: A DNA probe complementary to a predicted mRNA sequence can be used to locate and isolate the target mRNA strand. Once isolated, this mRNA can then be used as a template to synthesize its corresponding DNA (cDNA) in the laboratory, aiding in gene isolation for further study or manipulation.