B1.1 Genome and what does it do?

Genetic Material

• Structured into chromosomes, which consist of long DNA molecules containing genes.

• All organisms have genetic material that directs cell and organism development and function.

• Genetic instructions are encoded in DNA and influenced by environmental factors, leading to the organism's specific traits.

Location and Structure

• In eukaryotes (plants and animals), genetic material resides in the nucleus.

• Prokaryotes (bacteria) lack a nucleus, and their genetic material is found in the cytoplasm.

  • Plasmids play a significant role in expanding the functional capabilities of prokaryotic cells (bacteria and archaea). They are not essential for the basic survival of the cell, but they offer a set of advantages that can significantly enhance a cell's ability to thrive in different environments such as;

    • Extrachromosomal DNA: Plasmids are small, circular, extrachromosomal DNA molecules which exist independently of the chromosome within the cytoplasm.

    • Carrying Non-Essential Genes: Plasmids typically carry genes that code for non-essential, but often beneficial, functions. These genes can be broadly categorized into a few key areas:

      • Antibiotic Resistance

      • Toxin Production

      • Metabolic Versatility

      • Conjugation

Genome

• The genome is the entire set of genetic material in an organism.

  • Chromosomes within the genome are composed of long DNA strands with numerous genes.

The genome and environment play a complex but crucial duet in determining an organism's phenotype. It works like the following:

Genome Instruction

• Genes (Recipes): Think of your genome as a giant instruction manual containing recipes (genes) for building proteins, the building blocks of your body.

  • Each gene carries specific instructions that determine how these proteins are made.

• Variations and Complexity: These recipes can have variations (alleles).

  • Some variations might not affect the final product (protein), while others might change its function significantly (adding another layer of complexity).

Environmental Influence

• Turning Genes On and Off: The environment doesn't directly change the DNA sequence, but it can influence how genes are expressed.

  • Environmental factors like diet, light exposure, or stress can activate or deactivate certain genes, affecting which proteins are made and in what quantities.

• Nutrient Availability: The availability of nutrients in the environment can act like the specific ingredients needed in a recipe.

  • An organism might not be able to fully express a gene's instructions if essential nutrients are missing.

The Result

• Interaction is Key: The final phenotype is the result of the interplay between the genome (the instructions) and the environment (the modifiers).

  • Example - a gene might code for tall plants, but if the environment lacks enough sunlight or nutrients, the plants might grow shorter.

• Most Traits are Polygenic: Many traits, like eye color or height, are influenced by multiple genes interacting with the environment.

  • Examples:

    • Coat Color in Mammals - Some mammals have genes for coat color variations like brown or black.

      • But, cold temperatures can activate genes for melanin production, leading to a darker coat even if the "brown" allele isn't present.

    • Lactose Tolerance in Humans - The ability to digest lactose (milk sugar) as adults depends on a gene that normally gets switched off after infancy.

      • However, some populations with a history of dairy consumption in their diet have environmental pressure to maintain this gene's activity, leading to lactose tolerance.

Chromosomes and Genes

• Chromosomes: Are thread-like structures in the cell's nucleus that carry this genetic information made of DNA, which holds the instructions themselves.

  • Chromosomes in plants and animals are typically paired, one from each parent.

• Gene: Are specific sections of DNA within a chromosome where each gene acts like a recipe for a protein, which does a particular job in the cell.

  • Genes direct cells on how to build proteins, which involves linking amino acids in a specific order to form proteins.

  • Alleles: A different version of genes Think of these as variations on the same recipe.

    • Example - a gene for eye color might have a brown eye allele or a blue eye allele. (People inherit two alleles for each gene, one from each parent.)

  • Variant: A broader term which refers to any difference in the DNA sequence.

    • Not all variants affect genes or change traits.

Genotype vs. Phenotype

• Genotype: The specific alleles present in an organism for a particular gene.

• Phenotype: The observable trait or characteristic resulting from the genotype's interaction with the environment.

Importance of Amino Acids in Protein Synthesis

Amino Acids

• Serves as the building blocks of proteins.

• There are 20 different types, each with a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

  • R Group: The key player that varies in size, shape, and electrical properties, determining how the amino acid interacts with others and ultimately influencing protein function.

    • Example - a bulky hydrophobic side chain might repel water, making it suitable for interacting with lipids in cell membranes, while a charged side chain might be crucial for an enzyme to attract its target molecule.

The Genome

• Acts as the blueprint.

• The instructions for building proteins reside within the organism's DNA, specifically in its genes.

  • Each gene codes for a specific sequence of amino acids.

• 2 main steps in translating the code into a protein;

  1. Transcription: DNA in the nucleus is copied into a messenger RNA (mRNA) molecule.

     • mRNA acts as a mobile copy of the instructions, carrying the genetic code to the protein-building machinery in the cytoplasm.

  2. Translation: Ribosomes in the cytoplasm read the mRNA code.

     • Transfer RNA (tRNA) molecules, each carrying a specific amino acid, match their anticodons (complementary sequences) to the codons (triplets of nucleotides) on the mRNA.

     • Ribosomes link these amino acids together in the order specified by the mRNA, forming a polypeptide chain – the nascent protein.

Sequence to Structure

• The specific sequence of amino acids in a protein is critical as it dictates how the protein folds into its final 3D structure, which in turn determines its function.

  • Think of building a complex LEGO structure. The specific arrangement of the bricks defines the final outcome – a spaceship or a castle. Similarly, the amino acid sequence dictates how the protein folds, resulting in a unique 3D shape.

• Function Follows Form

  • The final 3D structure of a protein allows it to perform its specific function.

  • An enzyme with a precisely folded active site can bind its target molecule and catalyze a reaction.

  • A structural protein with a specific folded shape can provide support to tissues.

B1.2 How is genetic information inherited?

Definition of terms

• Gamete: Are reproductive cells, like sperm or egg cells, that carry half the genetic information (one set of chromosomes) an organism has.

• Homozygous: Refers to an organism having two identical alleles (versions of a gene) for a particular trait.

• Heterozygous: This describes an organism having two different alleles for a particular trait.

• Dominant: A dominant allele is one that masks the effect of a recessive allele for the same trait.

• Recessive: A recessive allele is only expressed when an organism has two copies of it (one from each parent). If paired with a dominant allele, the recessive trait will be masked.

Single Gene Inheritance

• Describes how a single gene with two possible alleles determines a particular trait in an offspring.

  • Alleles can be dominant or recessive, influencing how the trait is expressed.

Allele Inheritance

• Each offspring inherits two alleles for each gene, one from each parent.

  • Homozygous individuals have two copies of the same allele.

  • Heterozygous individuals have different alleles

  • Alleles can be dominant or recessive, influencing their expression in the phenotype.

Genetic Diagrams

• Family trees and Punnett squares are used to predict the inheritance patterns of single gene traits.

• These tools help in understanding how certain traits are passed from parents to offspring.

Mendelian Crosses

• Predicting the results of single gene crosses are known as Mendelian crosse.

• Involves understanding dominant and recessive alleles and using Punnett squares.

Steps

1. Identify the Trait and Alleles

   • Determine the trait you're interested in (e.g., pea pod color, seed shape).

   • Assign letters to represent the alleles:

     • Capital letter (e.g., A) for the dominant allele.

     • Lowercase letter (e.g., a) for the recessive allele.

2. Define Parental Genotypes

   • Determine the genotypes of the parent organisms.

     • They can be homozygous dominant (AA), homozygous recessive (aa), or heterozygous (Aa).

3. Draw the Punnett Square

   • Create a grid with two rows and two columns.

     • Label the top row with the alleles of one parent (e.g., Aa) and the left column with the alleles of the other parent (e.g., Aa).

4. Fill the Punnett Square

   • In each square, combine the alleles from the corresponding row and column.

     • Example - in a square where A meets a, the resulting genotype would be Aa.

5. Analyze the Offspring

   • Each square represents a 25% chance of that particular genotype appearing in the offspring.

   • Identify dominant and recessive phenotypes based on the alleles present.

Example:

• Trait: Pea pod color (Green = Dominant - G, Yellow = Recessive - g)

• Parents: P1 (Aa - Green) x P2 (Aa - Green)

Punnett Square:

Analysis:

• There is a 75% chance (3 out of 4) the offspring will have green pods (GG or Gg - dominant phenotype).

• There is a 25% chance (1 out of 4) of having yellow pods (gg - recessive phenotype).

Polygenic Inheritance

Definition: Are the phenotypic features that are the result of multiple genes rather than a single gene inheritance pattern. The following are the reasons why single-gene inheritance is less common than polygenic inheritance;

• Complex Traits: Many phenotypic features involve complex biological processes influenced by multiple genes working together.

  • Example - Eye color, height, and susceptibility to diseases like diabetes are all influenced by the interaction of several genes.

• Allelic Variation: Each gene can have multiple alleles, different versions of the gene that can code for slightly different traits.

  • The combination of alleles from both parents determines the overall outcome for a particular feature.

• Environmental Factors: Can also play a significant role in shaping phenotypic traits.

  • Factors like nutrition, exercise, and exposure to sunlight can influence characteristics like height, body composition, or skin pigmentation.

Sex Determination

A human individual’s sex is determined by the inheritance of genes located on sex chromosomes; specifically, genes on the Y chromosome trigger the development of testes.

B1.3 How can and should gene technology be used?

Importance of Medicine in Understanding Human Genome

1. Association of Diseases

• Identifying Genetic Risk Factors: By analyzing the human genome, scientists can identify specific genes and alleles associated with an increased risk of developing certain diseases. This knowledge allows doctors to:

  • Develop Risk Assessments: Individuals with a family history of a particular disease can undergo genetic testing to assess their personal risk based on their genetic makeup.

  • Early Detection: For diseases with a genetic component, early detection through genetic testing allows for preventive measures or earlier intervention, potentially leading to better outcomes.

2. Personalized Medicine

• Tailored Treatments: Understanding an individual's genetic makeup allows for a more personalized approach to treatment. Doctors can prescribe medications or therapies based on a patient's specific genetic profile, potentially increasing effectiveness and reducing side effects.

• Pharmacogenomics: This field studies how genes influence an individual's response to medications. By analyzing genetic variations, doctors can predict how a patient might metabolize a particular drug, allowing them to choose the most effective and safest treatment option.

3. Family Planning and Genetic Counseling

• Carrier Screening: Couples planning a family can undergo genetic testing to identify if they are carriers of specific genetic mutations that could be passed on to their children. This information allows them to make informed decisions about family planning and explore options like preimplantation genetic diagnosis (PGD).

• Genetic Counseling: Genetic counselors can interpret genetic test results and provide guidance and support to individuals and families facing genetic conditions.

Genetic Engineering

Definition: It is a process which involves modifying the genome of an organism to introduce desirable characteristics.

• It is used to introduce characteristics into organisms such as bacteria and plants that are useful to humans.

Steps in Genetic Engineering Process

1. Isolating and replicating the required gene(s)

   • Identifying the Target: The first step is to identify the specific gene(s) you want to introduce or modify.

     • It involves extensive research and understanding of the biological process you're trying to influence.

   • Extraction Techniques: Once the target gene is identified, scientists use specialized techniques to extract it from the donor organism's DNA.

     • Techniques may involve restriction enzymes that cut DNA at specific sequences.

   • Gene Replication: Since typically only a small amount of DNA is extracted, the desired gene needs to be replicated (amplified) using a technique like Polymerase Chain Reaction (PCR), creating multiple copies of the gene for further manipulation.

2. Putting the gene(s) into a vector (e.g. a plasmid)

   • Plasmid Power: A common vector used in genetic engineering is a plasmid, a small, circular DNA molecule found in bacteria.

     • Plasmids can be easily manipulated and replicate independently of the bacterial chromosome.

   • Introducing the Gene: Scientists use restriction enzymes and ligase enzymes to "cut and paste" the desired gene into the plasmid. creating a recombinant DNA molecule where the gene of interest is combined with the plasmid's DNA.

3. Using the vector to insert the gene(s) into cells

   • Into the Host: The next step involves introducing the recombinant plasmid containing the desired gene(s) into the host cells (the cells you want to modify).

     • This process called transformation, can be achieved through various methods like electroporation or chemical treatments that make the cell membrane temporarily permeable.

4. Selecting modified cells

   • Not All Cells Take Up the Plasmid: After transformation, not all host cells will successfully take up the recombinant plasmid.

     • Therefore, a selection process is employed to identify and isolate the cells that have been genetically modified.

   • Antibiotic Resistance Markers: Plasmids often carry genes for antibiotic resistance.

     • By growing the transformed cells in a medium containing the specific antibiotic, only cells that have taken up the plasmid (and thus the gene for resistance) will survive, allowing scientists to identify and isolate the genetically modified cells.

Gene Technology in Society

• Gene technology addresses societal needs by improving agricultural productivity and advancing medical treatments.

• Ethical considerations involve assessing the risks and benefits of genetic modifications, including potential long-term effects on ecosystems and human health.

• Moral concerns focus on the implications of genome modification and the need for thorough ethical deliberation.

Risks and Benefits of using Gene Technology in Modern Agriculture and Medicine

Agriculture

Ethical Considerations

• Environmental Impact: The potential long-term effects of GE crops on the environment need careful evaluation.

• Right to Food: Ensuring access to safe and affordable food for all is crucial, regardless of reliance on GE technology.

Medicine

Practical Considerations

• Regulations: Stringent regulations are needed to ensure the safety and ethical development of GE technologies in medicine and agriculture.

• Public Education: Open dialogue and education about the potential benefits and risks are crucial for informed decision-making.

• Long-Term Studies: Long-term studies are essential to fully understand the potential ecological and health impacts of GE technologies.