The basics of DNA

**Deoxyribonucleic Acid (DNA)**

- DNA forms the genetic material of living organisms.
- As Linda Geddes stated, understanding the human genome remains a complex challenge despite advancements.
- DNA consists of a sugar-phosphate backbone with four nitrogen-containing bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).
- Adenine pairs with Thymine, and Guanine pairs with Cytosine, forming a double helix structure.
- Chromosomes in the nucleus contain DNA and histone proteins, organizing genetic material.

**Chromosomes**
- The human genome comprises approximately 3 billion base pairs divided into 46 chromosomes.
- Somatic cells have pairs of chromosomes (diploid), while gametes are haploid, containing a single set of chromosomes.
- There are 22 pairs of autosomal chromosomes and one pair of sex chromosomes (XX for females, XY for males).
- Chromosomes are homologous, containing similar genetic information.

**Karyotype**
- Chromosomes are visualized through a karyotype, showcasing their structure and organization.

**Heterochromatin/Euchromatin**
- Heterochromatin is condensed chromatin, transcriptionally inactive, and contains large numbers of tandem repeats.

**Genes**
- Genes are coding regions of DNA responsible for producing proteins.
- They consist of exons (protein-coding) and introns (non-protein coding).
- Pseudogenes are non-functional genes.

**Nucleic Acid Structure**

- The Central Dogma describes the ow of genetic information from DNA to RNA to proteins.
- DNA consists of deoxyribonucleotide units linked by phosphate groups.
- Four nitrogenous bases (Adenine, Guanine, Thymine, Cytosine) are bonded to the sugar-phosphate backbone.

**DNA Bases**
- Adenine and Guanine are purines, while Thymine and Cytosine are pyrimidines.

**Nucleoside versus Nucleotide**

- Nucleoside: Base bonded to a sugar (Deoxyadenosine, Deoxyguanosine, Deoxythymidine, Deoxycytidine).
- Nucleotide: Nucleoside + Phosphate group.

**The Double Helix**

- DNA is double-stranded, with two antiparallel polynucleotide chains twisted into a helical structure.
- Adenine pairs with Thymine (2 H bonds), and Guanine pairs with Cytosine (3 H bonds).

**The Chargaff’s Rule**

- Discovered by Erwin Chargaff, states that the amount of A = T and C = G in DNA samples.

**RNA vs DNA**
- RNA contains Ribose sugar, is single-stranded, and uses Uracil instead of Thymine.
- DNA contains Deoxyribose sugar, is double-stranded, and uses Thymine.

**Must-Know Concepts**
- DNA structure (chromosome, gene), differences between DNA and RNA structures, speci c base pairing.
**Should-Know Concepts**
- Understanding Chargaff’s rule.
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A History of DNA Pro ling
**Key Figures and Milestones:**
- **1985**: Introduction of Multi Locus Probes (MLPs) by Prof. Alec Jeffreys.
- **1990**: Single Locus Probes (SLPs) become prevalent, providing faster results within a week.
- **1994**: Polymerase Chain Reaction (PCR) technology advances with the Quad system, allowing thousands of DNA pro les to be processed.
- **1995/7**: Introduction of Short Tandem Repeat (STR) technology (SGM) capable of analyzing DNA pro les from a million individuals.
- **1999**: SGM+ technology scales up to handle pro les from a billion individuals.
- **2014**: DNA17 and Global ler systems further enhance capacity to analyze pro les from a billion individuals.
- **Future**: Ongoing advancements in DNA pro ling techniques are anticipated.

**Core Concepts:**
- **DNA Variations**: DNA pro ling relies on variations in repeated sequences called 'core sequences' or 'alleles'.
- **Alleles**: Each variation is termed an allele, representing different types of a core sequence.
- **Inheritance**: Individuals inherit two alleles, one from each parent, at each locus (speci c position on a chromosome).
- **DNA Typing**: Techniques involve separating and typing repeat units, forming the basis of DNA pro ling.

**Historical Signi cance:**

- **First Legal Case**: The pivotal case involved two rape and murder incidents in Leicestershire (1983 and 1986), where DNA pro ling linked the same individual to both crimes.
- **Colin Pitchfork Case**: Colin Pitchfork became the rst individual convicted with the help of DNA pro ling. His DNA pro le matched semen samples from both murders, leading to a
life imprisonment sentence in 1988.
- **Discovery by Sir Alec Jeffreys**: Investigating the myoglobin gene, Jeffreys discovered a large intron with repeat sequences, laying the foundation for DNA pro ling.

**Evolution of Pro ling Techniques:**

- **Multi Locus Probes (MLPs)**: Introduced by Jeffreys, utilized restriction enzymes to create Restriction Fragment Length Polymorphisms (RFLPs), enabling discrimination but with
statistical limitations.
- **Single Locus Probes (SLPs)**: Offered faster results and easier interpretation by focusing on distinct non-coding areas of DNA, though still requiring large DNA samples.
- **PCR Technology**: Developed by Kary Mullis in 1983, PCR facilitated ampli cation of DNA segments, enhancing the speed and ef ciency of pro ling, particularly with Short
Tandem Repeat (STR) analysis.

**Understanding RFLP Technique:**

- **Restriction Fragment Length Polymorphisms (RFLPs)**: Detected variations in DNA sequences through gel electrophoresis, utilizing speci c restriction enzymes to cut DNA into
fragments of different lengths.
- **Restriction Enzymes**: DNA-cutting enzymes found in bacteria, recognized and cut DNA at speci c nucleotide sequences, producing either blunt or sticky ends.
- **Southern Blotting**: A technique used to transfer digested DNA onto a membrane for further analysis, enabling visualization of DNA fragments via labeling and hybridization.

**Applications of rDNA Technology:**

- **Recombinant DNA (rDNA)**: Enabled the production of various therapeutic products, including insulin, human growth hormone, and factors for treating hemophilia and anemia.

These detailed study notes cover the historical development, core principles, and technical aspects of DNA pro ling, providing a comprehensive understanding for learning and
reference.
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 DNA Extraction
**1. Importance of DNA Extraction:**
- DNA must be separated from other cellular components and non-biological material to ensure accuracy in downstream procedures.
- Foreign material and nuclease enzymes can degrade DNA, affecting its integrity and ef ciency in analyses.

**2. Factors Affecting DNA Extraction:**

- Source of DNA (blood, faeces, semen, saliva, hair), sample amount, cell types present, and quality needed for downstream applications in uence the isolation procedure.

**3. Ideal Forensic DNA Extraction Method:**

- Extracts DNA from various biological materials, even in small quantities.
- Yields high DNA concentration, removes substances interfering with PCR, avoids introducing inhibitors or contamination, maintains sample integrity, and is rapid and automatable.

**4. Examples of Biological Materials for DNA Extraction:**

- Blood, food samples, bacteria, semen, bones, teeth, hair (with root/shaft), saliva, urine, faeces, debris from ngernails, muscle tissue, cigarette butts, postage stamps, dandruff,
ngerprints, and personal items.

**5. Case Example:**

- DNA extracted from a leech helped solve a crime, emphasizing the diverse sources DNA can be obtained from for forensic analysis.

**6. Factors Leading to DNA Degradation:**

- Temperature, humidity, light, exposure to chemicals, and time can degrade DNA.

**7. Reasons for DNA Extraction and Puri cation:**

- DNA is con ned to organelles, enzyme reactions may be inhibited by compounds in cell lysate, and samples can be contaminated by surroundings.

**8. Potential Contaminants of DNA:**

- Nucleic acids, proteins, and lipids from cell contents can contaminate DNA samples.

**9. DNA Extraction Methodologies:**

- Phenol/chloroform, Chelex, silica-based commercial kits, and differential extraction are common methods, each with advantages and disadvantages.

**10. DNA Extraction Techniques:**

- Phenol/chloroform method involves lysing cells, separating organic and aqueous phases, and precipitating DNA with ethanol.
- Chelex method uses ion-exchange resin to bind metal ions and extract DNA, suitable for small samples and PCR analysis.
- Silica column extraction involves binding DNA to silica, washing off contaminants, and releasing puri ed DNA.

**11. Differential Extraction:**

- Used to separate sperm cells from other cells, involving speci c treatments to isolate sperm DNA.

**12. Automation of DNA Extraction:**

- Instruments like Qiagen EZ1 Advanced xl and Qiagen QIAcube automate DNA extraction, minimizing manual errors and ensuring uniformity.

**13. Considerations for DNA Extraction Protocols:**

- All protocols require proper handling, including considerations for additional samples, incubations, centrifugation, and reagent usage.

By understanding these key concepts and methods, you can effectively extract and purify DNA for various applications in forensic science and research.
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Quanti cation of DNA
**Methods:**

1. **Real-Time PCR (qPCR)**

- Utilizes uorescent dye binding to double-stranded DNA during PCR.
- Can target any speci c region of template DNA.
- Commercial kits available like Quanti ler systems and HY Plexor system.
- Advantages: Very sensitive, accurate, human-speci c (and Y-speci c), assesses DNA sample quality.
- Disadvantages: Requires expensive equipment.

2. **Fluorometry**
- Utilizes uorescent dyes like PicoGreen or SYBRGreen.
- More sensitive than UV absorbance methods.
- Requires a standard curve for accurate quanti cation.
- Advantages: Sensitive, rapid, can be automated.
- Disadvantages: Not species-speci c, quanti es only dsDNA, uses a lot of sample.

3. **Slot Blot**
- Involves immobilizing DNA on a nylon membrane and hybridizing it with a complementary probe.
- Quantity determined by comparing band intensities to standard DNA dilutions.

4. **UV Spectrophotometry**
- Measures absorbance/transmission of light through a liquid.
- Utilizes A260/A280 ratio as an indicator of DNA purity.
- A260 reading used to calculate DNA concentration.
- Advantages: Quick and easy.
- Disadvantages: Not very accurate, protein and RNA interference, not species-speci c, uses a lot of sample, not sensitive enough.

5. **Agarose Yield Gel**

- Semi-quantitative/qualitative assay estimating DNA concentration and quality.
- Electrophoresis of DNA in agarose gel matrix with uorescent dye.
- Concentration determined by comparing uorescence intensity to calibration standards.

**Purpose of Quanti cation:**

- Determines exact amount of human DNA present in DNA extracts.
- Downstream PCR requires approximately 1ng (1 billionth of a gram).
- Results reported in ng/µl.

**Notes:**
- Real-time PCR offers high sensitivity and accuracy, with the ability to assess DNA sample quality, but it requires expensive equipment.
- Fluorometry, particularly using PicoGreen, is highly sensitive and rapid, making it suitable for quantifying low concentrations of DNA, such as those needed for next-generation
sequencing.
- UV Spectrophotometry provides quick results but may lack accuracy and speci city, especially regarding species identi cation.
- Agarose yield gels are cost-effective and assess DNA sample quality but may not provide precise quanti cation.
- Slot blotting combines immobilization of DNA on a membrane with hybridization for quanti cation, offering another method for DNA quanti cation.
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DNA replication and transcription
DNA Replication
**Principle of DNA Replication:**
- DNA replication involves the synthesis of new DNA strands using existing DNA strands as templates.
- Each strand of the double helix serves as a template for the formation of a new complementary strand.
- The process results in two daughter molecules, each containing one old strand and one newly synthesized strand.

**Semi-Conservative Replication:**
- Three possible replication models: Conservative, Semi-Conservative, Dispersive.
- Meselson and Stahl's experiment demonstrated semi-conservative replication.
- They labeled DNA with heavy nitrogen (15N) and then switched to light nitrogen (14N) to track the replication process.

**Steps of DNA Replication:**

1. Initiation: DNA unwinds at the origin of replication, forming replication forks.
2. Elongation: New DNA strands are synthesized by DNA polymerases using the parental DNA as a template.
3. Termination: Replication is completed when replication forks meet or when speci c termination signals are encountered.

**Enzymes Involved in DNA Replication:**

- Helicases unwind the DNA strands.
- Single-stranded binding proteins stabilize the unwound DNA.
- DNA gyrase introduces negative supercoils to prevent tangling.
- Primase synthesizes RNA primers.
- DNA polymerases add nucleotides to the growing DNA strand.
- DNA ligase joins Okazaki fragments on the lagging strand.

**Prokaryotic vs. Eukaryotic DNA Replication:**

- Prokaryotes have a single origin of replication, while eukaryotes have multiple origins.
- Prokaryotic replication is faster, with DNA polymerase III adding 1000 nucleotides per second compared to DNA polymerase I in prokaryotes.
- Telomerase, which maintains telomeres, is present only in eukaryotes.

Transcription:

**Principle of Transcription:**
- Transcription is the process of synthesizing RNA from a DNA template.
- RNA polymerase catalyzes the synthesis of RNA using DNA as a template.
- In eukaryotes, transcription occurs in the nucleus, while translation (protein synthesis) occurs in the cytoplasm.

**Steps of Transcription:**
1. Initiation: RNA polymerase binds to the promoter region of the DNA.
2. Elongation: RNA polymerase synthesizes RNA using one strand of the DNA as a template.
3. Termination: Transcription stops when speci c termination signals are encountered.

**Prokaryotic Transcription:**
- RNA polymerase in prokaryotes consists of multiple subunits, including sigma factors that recognize promoter sequences.
- Transcription initiation requires recognition of promoter sequences such as the -10 (Pribnow box) and -35 sequences.

**Eukaryotic Transcription:**
- Eukaryotes have three RNA polymerases that transcribe different classes of RNA.
- Promoters in eukaryotes contain TATA boxes and additional regulatory sequences.
- Transcription factors regulate transcription by binding to enhancer and silencer sequences.

**Post-Transcriptional Modi cations:**

- RNA undergoes modi cations such as capping at the 5' end, polyadenylation at the 3' end, and splicing to remove introns.
- These modi cations ensure proper functioning and stability of the RNA molecules.

**Differences Between Prokaryotic and Eukaryotic Transcription:**

- Prokaryotes have a simpler transcription apparatus with a single RNA polymerase, while eukaryotes have three RNA polymerases.
- Promoters in prokaryotes have speci c sequences (-10 and -35 sequences), while eukaryotic promoters contain additional regulatory elements.
- Transcription and translation are coupled in prokaryotes but separated in eukaryotes.

**Key Concepts:**
- Semi-conservative Replication, Transcription Steps, Enzymes involved in DNA Replication, Nick Translation, Telomeres, Differences between prokaryotic and eukaryotic replication/
transcription.
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The Genetic Code and Translation
**The Central Dogma:**
- DNA → mRNA → Protein:
- Genes in DNA encode Proteins.
- DNA sequence indirectly determines the Amino acid sequence of Proteins.
- The Genetic Code acts as the link between DNA and proteins.

**Understanding the Genetic Code:**

- Codons:
- Triplets of bases that code for speci c Amino Acids.
- Each Amino Acid is encoded by at least one codon.
- Bases and Amino Acids:
- DNA has four bases, leading to 64 possible codons (4^3).
- Degeneracy: Some Amino Acids are speci ed by multiple codons.
- Start and Stop Codons:
- AUG codes for N-formyl methionine, serving as the start codon.
- UAG, UGA, and UAA are stop codons.
- Exercise: Transcribe and translate DNA sequences to determine mRNA and amino acid sequences. Predict effects of mutations on protein sequence.

**Degeneracy and Multiple Codons:**

- Some Amino Acids have multiple codons.
- Nucleotide substitutions can lead to silent mutations.
- Some codons mark the start and end of genes.
- Base Pair Wobble: Loose base pairing between codons and anticodons.

**Non-overlapping Genetic Code:**

- Single base mutations typically lead to single amino acid changes.
- Overlapping codes could result in multiple amino acid changes due to mutations.
- The Genetic Code is read from a xed starting point and continues to the end of the coding sequence.
- Frameshift mutations alter codon alignment, affecting translation.

**Types of RNA in Cells:**

- Messenger RNA (mRNA): Template for protein synthesis.
- Transfer RNA (tRNA): Carries activated amino acids to ribosomes.
- Ribosomal RNA (rRNA): Major component of ribosomes.
- Small Nuclear RNA (snRNA): Participates in RNA splicing in eukaryotes.

**Translation Process:**
- Protein Synthesis:
- Amino acids are assembled into polypeptide chains.
- mRNA speci es the amino acid sequence.
- Ribosomes:
- Composed of rRNA and proteins.
- Bacterial and eukaryotic ribosomes have different sedimentation coef cients.
- tRNA Features:
- Clover-like structure, with unique loops and sequences.
- Recognizes codons on mRNA and carries speci c amino acids.
- Amino Acid Activation:
- Amino acids are activated by speci c enzymes before attaching to tRNA.
- Codon-Anticodon Interactions:
- Base pairing between codons and anticodons ensures accurate translation.
- Degeneracy arises from imprecision in the pairing of the third base of the codon.

**Components Needed for Translation:**

- Amino acids, ribosomes, mRNA, tRNA, enzymes, ATP, GTP, initiation factors, and various inorganic cations are essential for protein synthesis.

**Translation Steps:**
1. Initiation:
- mRNA binds to the ribosome, initiating protein synthesis.
- Initiator tRNA brings methionine to the ribosome.
2. Elongation:
- Amino acids are added to the growing polypeptide chain.
- Peptide bond formation and translocation occur.
3. Termination:
- Protein synthesis stops when a stop codon is reached.
- Release factors hydrolyze the bond between the polypeptide chain and tRNA.
- Ribosome dissociates into subunits.
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**Summary of Translation:**
- Amino acids are activated, transferred to tRNA, and assembled into polypeptide chains.

- Ribosomes read mRNA and catalyze peptide bond formation during translation.
- Codon-anticodon pairing ensures accuracy in protein synthesis.

**Key Concepts:**
- Understanding the Genetic Code and Translation is crucial for comprehending protein synthesis mechanisms and genetic variations.
Types and forms of DNA
**Genome:**
- De nition: The sum total of all genetic material within an individual.
- Function: Provides comprehensive information about the organism and directs vital processes, including coding and non-coding regions.
- Locations: Found in the nucleus (nuclear DNA) and mitochondria (mitochondrial DNA).

**Types of DNA:**
- **Nuclear DNA:**
- Location: Situated within the nucleus of eukaryotic cells.
- Copy Number: Typically two copies per cell.
- Structure: Linear chromosomes with open ends, totaling 46 chromosomes containing 3 billion nucleotides.
- Inheritance: Diploid, inheriting DNA from both parents.
- Mutation Rate: Less than 0.3%.

 (Karyotype - Week 1)

- **Mitochondrial DNA (mtDNA):**

- Location: Located in the mitochondria.
- Copy Number: Ranges from 100 to 1,000 copies per cell.
- Structure: Circular chromosomes, for example, 16,569 nucleotides in humans.
- Inheritance: Haploid, inherited solely from the mother.
- Mutation Rate: Generally higher than nuclear DNA.

- **Chloroplast DNA (cpDNA):**

- Location: Found within the chloroplast.
- Alias: Sometimes referred to as plastosome.
- Copy Number: Varies from 100 to 1,000 copies per cell.
- Structure: Typically circular, larger, and more complex than mtDNA, with around 120 genes.
- Length: Consists of base pairs ranging from 120,000 to 170,000.
- Segregation: Randomly segregated.
- Function: Encodes proteins and RNAs essential for functions such as photosynthesis.

**Forms of DNA:**
- **Classic Watson-Crick Model (B-DNA):**
- Description: Predominant form of DNA.

- **Other Forms:**
- A-DNA, Z-DNA, C-DNA, D-DNA, E-DNA.
- These forms vary based on structural diversity under speci c conditions.

**Key Points to Remember:**

- Understanding the different types of DNA and their respective locations.
- Familiarity with the various forms of DNA and their structural diversity.
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Revision of Mendelian Genetics
**Figure 14.0: Painting of Mendel**

**Mendelian Genetics: Understanding the Legacy of Gregor Mendel**

- Gregor Mendel: An Augustinian monk, pioneering the study of inheritance at the University of Vienna.
- Focus on pea plants: The cornerstone of Mendel’s investigations due to their varied heritable characters.

**Mendel’s Peas: Unveiling the Mechanisms of Inheritance**

- Each trait inheritance governed by "units" or "factors" (later known as genes).

- Individuals inherit one unit from each parent for every trait, which may not manifest but can be passed down.
- Mendel’s groundbreaking three-generation studies revealed:
- The Law of Segregation.
- The Law of Independent Assortment.

**Genotype: The Blueprint of Inheritance**

- Genotype: Consists of discrete, heritable units known as genes, residing at speci c loci on chromosomes.
- Chromosomal sequences de ne genotype, transferred from parent to offspring.

**Phenotype: The Observable Outcome**

- Phenotype mirrors genotype but may vary due to complex interactions.

- Examples include hair color, height, etc., with multiple genotypes for one phenotype.
- Dominance principles dictate expressed traits: Dominant vs. recessive alleles.

**The Law of Segregation: Unraveling Allelic Distribution**

- Alleles for a character segregate into separate gametes, uniting randomly during fertilization.
- Accounts for observed 3:1 phenotypic ratio in the F2 generation.
- Mendel’s diagrams elucidate the Law’s principles.

**The Law of Independent Assortment: Deciphering Allelic Freedom**

- Allele pairs segregate independently, manifesting in dihybrid crosses.

- Depicted through dihybrid cross experiments.
- Re ects probability laws akin to random chance events.

**Incomplete Dominance and Codominance: Complexity in Phenotypic Expression**

- Incomplete dominance: Intermediate phenotype results when neither trait dominates.

- Codominance: Both alleles in uence phenotype distinctly.
- Examples include snapdragon ower color and ABO blood types.

**Pleiotropy and Polygenic Inheritance: Multifaceted Genetic In uence**

- Pleiotropic genes in uence multiple phenotypic traits.

- Polygenic inheritance involves multiple genes contributing to a single phenotype.
- Illustrations include coat color in mice and human skin color.

**Environmental In uence on Phenotype: The Intersection of Nature and Nurture**

- Phenotype in uenced by both genetic makeup and environmental factors.

- Demonstrated in examples like litmus owers, showcasing color changes based on soil acidity.

**Human Genetics and Mendelian Inheritance**

**AS2903 - Dr. Emma Hector**

**Summary and diagrams from: CAMPBELL BIOLOGY. 9TH EDITION, Pearson**

**Mendelian Inheritance in Humans**

**1. Pedigree Analysis: Unveiling Human Inheritance Patterns**

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- Pedigree analysis deciphers inherited traits across generations.
- Information collated to map phenotypic distribution in family trees.
- Utilized to predict genotypes based on observed phenotypes.

**2. Human Disorders: Manifestations of Mendelian Laws**

- Thousands of genetic disorders follow Mendelian inheritance patterns.

- Ranging from mild to severe, these disorders often exhibit recessive traits.
- Illustrations include albinism and cystic brosis.

**Understanding Recessive Alleles and Inherited Disorders**

- Recessive alleles manifest disorders when present in homozygous individuals.

- Heterozygotes exhibit normal phenotype but can transmit alleles to offspring.
- Genetic disorders re ect varied distributions in uenced by historical genetic isolation.

By incorporating detailed explanations, illustrations, and real-world examples, these enhanced lecture notes aim to provide comprehensive insight into Mendelian genetics and its
applications in understanding human inheritance patterns and genetic disorders.
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Human Genetic Disease
**Monogenic Disease:**
- Modi cation in a single gene occurring in all cells of the body.
- Can be as minor as a single nucleotide error.
- Examples: Cystic brosis, Tay-Sachs disease, Sickle-cell disease.
- Over 10,000 known human diseases.

**Classi cation:**
- Dominant
- Recessive
- X-linked

**Recessive Inherited Disorders:**

- Cystic Fibrosis (CF):
- Affects respiratory, digestive, and reproductive systems.
- Symptoms: Thick mucus in lungs, pancreatic obstructions.
- Most common mutation: Trinucleotide deletion.
- Incidence: Affects 1 in every 2,500 Caucasians of European descent.

**Cystic Fibrosis (Continued):**

- Normal allele codes for CFTR membrane protein, regulating Cl- transport.
- Defective channels lead to thick, sticky mucous build-up, causing infections.
- Without treatment, affected children die before ve, but with treatment can live past their late 20s.

**Tay-Sachs Disease:**
- Lethal recessive disorder.
- Dysfunction of Hexosaminidase A enzyme, leading to lipid accumulation in the brain.
- Symptoms: Onset with seizures, blindness, degeneration of motor and mental performance.
- Higher incidence among Ashkenazi Jews (1 in 3,600 births).

**Sickle-Cell Disease:**
- Most common among African Americans.
- Caused by single amino acid substitution in haemoglobin.
- Low oxygen levels cause sickling of RBCs, leading to various symptoms.
- Heterozygotes exhibit sickle-cell trait, which offers resistance to malaria.
- Treatments: Blood transfusions, new drugs.
- Incompletely dominant at organism level, codominant at molecular level.

**Dominant Inherited Disorders:**

- Examples: Achondroplasia (dwar sm).
- Incidence: One case in 10,000 people.
- Heterozygotes show phenotype, homozygotes are lethal.

**Lethal Dominant Alleles:**

- Less common than lethal recessives.
- May escape elimination if they cause death after reproduction age.
- Example: Huntington’s Disease.

**Multifactorial Diseases:**
- Genetic component + environmental in uence.
- Examples: Heart disease, diabetes, cancer.
- Typically polygenic with complex inheritance patterns.
- Public health strategy: Focus on education about environmental factors and healthy lifestyle.

**Polygenic Disease:**
- Caused by combined actions of multiple genes.
- Examples: Heart disease, diabetes.
- Not inherited in simple Mendelian patterns.
- Strong environmental component.
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Screening & Counselling Notes
**Summary and Diagrams from: CAMPBELL BIOLOGY, 9th Edition**

#### Pedigree Symbols: Drawing a Family Pedigree

- Nigel has three children and a grandson.

- Represent Nigel and his wife, Margaret.
- Traditional placement: women on the right, males on the left.
- Add Nigel and Margaret’s children: Harry, Mary, and Elizabeth.
- Draw a vertical line from the center of the relationship line.
- Add a comb-like structure with three teeth pointing down for the children.
- Nigel and his middle daughter, Mary, both have achondroplasia (restricted growth).
- Shade in symbols for Nigel and Mary, including a key.
- Mary's son, Sam, also has achondroplasia; add him and his father, James, to the pedigree.


#### Technology in Genetic Testing and Counselling

- New tools for genetic testing and counselling.

- Preventative approach to simple Mendelian disorders.
- Risk assessment before conception or early in pregnancy.
- Hospitals offer genetic counsellors for prospective parents.

#### Genetic Counselling

- Consider hypothetical couple John and Carol.

- Both families have a recessive lethal disorder.
- Probability calculations for carrier status and disease occurrence in offspring.

#### Preconception Counselling

- Most children with recessive disorders born to phenotypically normal parents.

- Identifying carrier status is crucial.
- Recent tests distinguish carriers from homozygous dominants.
- Issues of con dentiality, discrimination, and counselling arise.

#### Preconception Testing

- Tests analyzing polar bodies or blastomeres for genetic disorders.

- Polar body technique: salvaging and analyzing chromosomes.
- Testing procedures for single gene disorders and chromosomal aneuploidies.

#### Embryo Biopsy - Blastomere Testing

- Removing cells from a 6- to 8-celled embryo for genetic diagnosis.

#### Post-Conception Testing

- Tests during pregnancy: amniocentesis and chorionic villus sampling (CVS).

- Foetal cells cultured and karyotyped from amniotic uid.
- Ultrasound and foetoscopy allow visual assessment of foetal health.
- Complications in about 1% of cases, including maternal bleeding or foetal death.

#### Genetic Screening

- Routine tests at birth for inherited disorders like phenylketonuria (PKU).

#### "3 Parent" Babies

- UK legalized embryos containing genetic material from three people.

- Aim: prevent maternal transmission of faulty mitochondrial DNA (2015).
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Human pedigree
**Factors to Consider in Pedigrees:**
- **Trait Location:** Determine if the trait is on a sex chromosome or an autosome.
- **Autosomal:** Not on a sex chromosome.
- **Sex Linkage:** Located on one of the sex chromosomes.
- **Y-linked:** Only males carry the trait.
- **X-linked (Recessive):** Sons inherit the disease from normal parents.
- **Trait Expression:**
- **Dominant:** The trait is expressed in every generation.
- **Recessive:** Expression of the trait may skip generations.

**Marfan’s Syndrome: An Example**

- Expressed in both sexes, hence autosomal.
- Expressed in every generation, thus dominant.
- **Genotyping:**
- **Normal Individuals:** "mm"
- **Affected Individuals:** At least one "M"

**Albinism: An Example**
- Expressed in both sexes at equal frequency, indicating autosomal.
- Not expressed in every generation, suggesting recessive.
- **Genotyping:**
- **Affected Individuals:** Homozygous for "a."
- **Normal Individuals:** At least one "A"

**Hairy Ears: An Example**

- Only males affected, indicating Y-linked inheritance.
- All sons of an affected father have hairy ears.
- **Genotyping:**
- **Gene on the Y Chromosome:** "H"
- **Wild-Type Allele:** "+"

**Haemophilia A: An Example**
- Only males affected, and sons do not share phenotypes with fathers, indicating X-linked.
- Expression skips generations, thus recessive.
- **Genotyping:**
- **Affected Individuals:** Have "H" on X chromosome.
- **Normal Individuals:** Have at least one X with "+"

**Mendelian Disorders:**
- X-linked inheritance and exceptions discussed.
- X-linked dominant disorders are rare.
- Male-to-male transmission of X-linked disorders does not occur.
- Carrier females may exhibit mild to moderate symptoms.

**Exceptions to Mendelian Inheritance: Human Mitochondrion**

- Inherited through the egg due to maternal transmission.
- Relatively few human genetic diseases caused by mitochondrial mutations.
- Distinctive pattern of inheritance.
- Usually evident as ATP synthesis de ciency.

**Mitochondrial Inheritance Pedigree:**

- All children of an affected female inherit the disease, while none of the children of an affected male will inherit it.
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Sex Chromosomes & Sex Determination
**Sex Chromosomes:**
- Females: Two X chromosomes.
- Males: One X chromosome and one Y chromosome.
- Presence of Y chromosome decisive for male phenotype.
- Up to 5 X chromosomes can still result in a male phenotype.

**The Y Chromosome:**
- During meiosis, X and Y chromosomes separate like homologous autosomes.
- X and Y chromosomes synapse during prophase I due to a small homologous region.
- Synapsis occurs in pseudoautosomal regions.

**Pseudoautosomal Regions:**
- Pairing of X and Y chromosomes during prophase I.
- Crossing over occurs in pseudoautosomal regions (PAR1 and PAR2).
- PAR1: 24 genes (deletion leads to sterility).
- PAR2: 4 genes.

**Genes outside Pseudoautosomal Regions:**

- 95% of Y chromosome located between pseudoautosomal regions.
- Around 80 genes identi ed.
- Some genes encode proteins used universally, while others function speci cally in testes.
- Key gene: SRY (sex-determining region Y).

**SRY:**
- Located on short arm of Y chromosome.
- Triggers developmental events leading to male phenotype.
- Absence results in female development.

**Evidence of SRY's Role:**

- Aneuploid humans with extra X chromosomes still phenotypically male.
- Transgenic mice with XX karyotype exhibit male phenotype when carrying SRY.

**Other Rarities:**
- XX individuals with testicular tissue due to translocation of SRY.
- XY females due to destructive mutation in SRY.
- Olympic testing for SRY gene.

**X Chromosome and Linkage:**

- X chromosome carries numerous genes unrelated to sex.
- Special rules due to X chromosome inheritance in males and females.
- Genes on X chromosome expressed in males even if recessive.

**Dominant X-linked Mutations:**

- Rare conditions like vitamin D-resistant rickets.
- Generally less severe in females due to X inactivation.

**Fragile X Syndrome:**
- Inheritance not strictly recessive or dominant.
- Linked to chromosome breakage site.
- Triplet repeat expansion leads to gene inactivation.
- Phenotypes vary in affected males and carrier females.

**X-Inactivation:**
- Females inherit two X chromosomes but only one remains active.
- Mechanism ensures dosage compensation.
- XIST gene plays a crucial role in X inactivation.
- XIST RNA accumulation leads to inactivation of one X chromosome.

**DNA Methylation:**
- Methylation of XIST regulatory sequences shuts down XIST expression.
- Allows continued expression of other X-linked genes.
- Creates genetic mosaics with varying gene content.

**Genetic Mosaics:**
- Result from X-inactivation.
- Cells with differing gene content and trait expression within an organism.
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**Calico Cats:**
- Display mosaic coat coloration due to X-linked genes.

- X inactivation determines coat color patches.

- Males express whichever color gene present on their single X chromosome.
- Male calicos rare, usually due to genetic defects.

**Anhydrotic Dysplasia Xq12-Xq13.1:**

- X-linked recessive disease.
- Absence of sweat glands.
- Normal males XY, affected males X'Y (no sweat glands).
- Heterozygous females XX' have patches of skin with and without sweat glands.
- Homozygous affected females X'X' lack sweat glands.
Sex Chromosome Abnormalities
**X-Chromosome Aneuploidy:**
Individuals may exhibit abnormal numbers of X chromosomes, a condition known as X-chromosome aneuploidy. Unlike most cases of aneuploidy, where the effects can be lethal, the
phenotypic consequences of X-chromosome aneuploidy tend to be less severe.

**Turner Syndrome:**
Turner Syndrome is characterized by females inheriting only one X chromosome, resulting in a genotype of X0. However, it's now recognized that many individuals with Turner
Syndrome exhibit mosaicism or have an additional X chromosome with a small inactive region. Those who survive to birth often present with abnormal growth patterns, including short
stature, typically around 4 foot 7 inches as adults. Distinctive physical features such as webbed necks, small jaws, high-arched palates, and underdeveloped ovaries are common.
They lack prominent female secondary sexual characteristics, with small, widely spaced breasts, broad shield-shaped chests, and turned-out elbows. Ovaries do not develop normally,
leading to infertility and an early onset of menopause. There's also an increased risk of thyroid disease and a potential reduction in IQ.

**Turner Syndrome Phenotype:**

Classic features of Turner Syndrome include a short webbed neck, turned-out elbows, and lymphoedema.

**Hormonal Therapy in Turner Syndrome:**

Although rare, Turner Syndrome affects approximately 1 in 3,000 to 1 in 5,000 female infants. Early diagnosis allows for treatment with regular injections of human growth hormones to
increase stature and estrogen replacement therapy to promote breast development and menstruation. These interventions help affected individuals appear relatively normal.

**Health Problems Associated with Turner Syndrome:**

Turner Syndrome individuals are prone to various health issues, including heart problems such as heart defects, abnormalities in heart structure, aortic dissection, aortic valve
stenosis, and increased risk of diabetes and high blood pressure. Hearing loss is common, often due to gradual nerve function loss and skull abnormalities. Kidney malformations,
immune system disorders, dental problems, vision issues, skeletal problems like scoliosis and osteoporosis, pregnancy complications, and psychological issues such as low self-
esteem, depression, anxiety, and ADHD may also arise.

**Meta-females or Triple-X Females:**

Meta-females have a genotype of XXX, XXXX, or XXXXX. They are typically slightly taller than average with normal sexual development and fertility. Some may experience slight
learning dif culties.

**Klinefelter Syndrome - XXY:**

Males with Klinefelter Syndrome inherit one or more extra X chromosomes, resulting in a genotype of XXY, XXXY, XXXXY, or XY/XXY mosaic. Features include high-pitched voice,
feminine body contours, breast enlargement, small testes and prostate gland, low testosterone levels, and infertility. Testosterone therapy can alleviate symptoms, but affected
individuals may still experience learning dif culties, overweight, and increased risk of osteoporosis, diabetes, and autoimmune disorders.

**XYY Syndrome:**
Males with XYY Syndrome inherit an extra Y chromosome, resulting in a genotype of XYY. They are usually tall with high testosterone levels. During adolescence, they may have acne
and coordination issues. While typically fertile and leading normal lives, they may be unaware of their chromosomal abnormality. Early studies erroneously linked XYY Syndrome to
aggression and low intelligence, exempli ed by the Richard Speck case. However, research suggests that high testosterone levels in XYY men may slightly increase the propensity for
violence.
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Sex-linked Inheritance
#### Overview of X-linked Diseases

**X-linked diseases** are genetic disorders caused by mutations in genes located on the X chromosome. As males have only one X chromosome (XY), they are more commonly
affected by X-linked disorders than females, who have two X chromosomes (XX).

#### Adrenoleukodystrophy (ALD)

- **Type**: X-linked recessive disorder.

- **Symptoms**: Progressive degeneration of the adrenal glands and white matter of the brain and spinal cord.
- **Inheritance Pattern**:
- Typically expressed in males.
- Sons of carrier females have a 50% chance of being affected.
- Affected males do not pass the trait to their sons.
- **Generational Skipping**: ALD often skips generations due to carrier females passing the mutated X chromosome to their sons.
- **Genetic Basis**: Mutations in the ABCD1 gene on the X chromosome.

#### Red-Green Color Blindness

- **Type**: Recessive X-linked trait affecting color vision.

- **Prevalence**: More common in males.
- **Genetic Basis**:
- Due to mutations in the red and green opsin genes located on the X chromosome.
- Individuals with red-green color blindness lack functional red or green cone cells in the retina.
- **Perception of Color**:
- Affected individuals perceive only red and blue colors instead of the full spectrum.
- Visual demonstration with color plates helps diagnose color blindness.

#### Genetics of Color Vision

- **Trichromatic Vision**:
- Normal vision involves the perception of red, green, and blue colors.
- Mediated by three types of cone cells in the retina, each containing different opsins sensitive to speci c wavelengths of light.
- **Opsin Genes**:
- Rhodopsin gene located on chromosome 3.
- Red and green opsin genes located on the X chromosome.
- Blue opsin gene located on chromosome 7.
- Mutations in these genes lead to various forms of color blindness.

#### Duchenne Muscular Dystrophy (DMD)

- **Type**: Rare X-linked recessive disorder.

- **Incidence**: Affects approximately 1 in 3600 males.
- **Symptoms**: Progressive muscle weakness and degeneration due to mutations in the dystrophin gene.
- **Outcome**: Death usually occurs by age 25 from respiratory failure.
- **Inheritance**: Passed from carrier females to affected sons.

#### X-linked Severe Combined Immunode ciency (X-SCID)

- **Type**: X-linked recessive disorder affecting the immune system.

- **Symptoms**: Prone to recurrent and persistent infections, which can be life-threatening.
- **Genetic Basis**: Mutations in the IL2RG gene on the X chromosome.
- **Outcome**: Without treatment, affected males usually do not survive infancy.

#### Congenital Generalized Hypertrichosis

- **Type**: X-linked dominant trait causing excessive hair growth.

- **Inheritance Pattern**:
- Daughters inherit from their fathers.
- Both daughters and sons can inherit from their mothers.
- **Historical Interest**: Potential connection to werewolf myths.
- **Research Interest**: Understanding its genetic basis sheds light on human evolution and hair loss.
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#### List of X-linked Conditions
- A comprehensive list of X-linked conditions includes various disorders such as:
- X-linked adrenoleukodystrophy

- X-linked sideroblastic anemia

- X-linked dystonia-parkinsonism
- X-linked severe combined immunode ciency
- And many more, each with unique genetic and clinical features.

#### Y-linked Genes

- **Examples**:
- SOX21 associated with baldness.
- Genes related to sex determination, fertility, and potential heart problems.

#### Conclusion

Understanding the complexities of sex-linked inheritance is essential for medical diagnosis, treatment, and genetic counseling. Research in this eld continues to unveil insights into
human genetics and evolution.
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Tutorial questions
Tutorial Questions:
1. Explain the structural components of DNA and the base pairing rules that govern its double helix structure.
2. What are chromosomes and how are they organized within the nucleus? Describe the difference between somatic cells and gametes in terms of chromosome numbers.
3. How are chromosomes visualized through karyotyping? What information does a karyotype provide about genetic material?
4. Describe the differences between heterochromatin and euchromatin in terms of chromatin structure and transcriptional activity.
5. De ne genes and explain their role in producing proteins. Differentiate between exons and introns in gene structure.
6. What are nucleosides and nucleotides, and how are they related in the context of DNA structure?
7. Explain Chargaff's rule and its signi cance in understanding the base composition of DNA.
8. Compare and contrast DNA and RNA structures in terms of sugar type, strand number, and base composition.
9. What is the central dogma of molecular biology, and how does it explain the ow of genetic information between DNA, RNA, and proteins?
10. De ne and differentiate between purines and pyrimidines in DNA bases.
11. Discuss different methods used for DNA quanti cation, such as real-time PCR, uorometry, slot blot, UV spectrophotometry, and agarose yield gel.
12. Describe the process of DNA replication, including initiation, elongation, and termination. Highlight the role of various enzymes involved in the replication process.
13. Explain the steps of transcription, including initiation, elongation, and termination. Discuss the differences between prokaryotic and eukaryotic transcription processes.
14. What is the genetic code, and how does it relate DNA sequences to protein synthesis? Explain the concepts of codons, start/stop codons, and degeneracy in the genetic code.
15. De ne and give examples of Mendelian genetics principles, such as the Law of Segregation and the Law of Independent Assortment. Illustrate these principles with examples from
Gregor Mendel’s experiments with pea plants.
16. How do pedigree analysis and genetic counseling help in understanding and predicting inheritance patterns of genetic disorders in families?
17. Discuss the importance of DNA extraction methods in genetics research and forensics. Explain the signi cance of the factors affecting DNA extraction and the various biological
materials that can be used for extraction.
18. Explain the different types and forms of DNA, including nuclear DNA, mitochondrial DNA, and chloroplast DNA. Discuss the structural and functional characteristics of these types
of DNA.
19. Discuss the inheritance patterns and clinical features of genetic disorders such as Cystic Fibrosis, Tay-Sachs Disease, and Sickle-Cell Disease.
1. Describe the genetic basis, symptoms, and inheritance patterns of X-linked diseases such as Adrenoleukodystrophy (ALD), Red-Green Color Blindness, Duchenne Muscular
Dystrophy (DMD), and X-linked Severe Combined Immunode ciency (X-SCID).

Tutorial answers
Exam Answers:
1. The structural components of DNA consist of a double helix made up of nucleotides. Each nucleotide comprises a sugar-phosphate backbone and nitrogenous bases. Adenine pairs
with Thymine, and Guanine pairs with Cytosine, forming the base pairing rules that stabilize the double helix structure.

2. Chromosomes are thread-like structures made of DNA and proteins found in the nucleus. Somatic cells are diploid, with pairs of chromosomes, while gametes are haploid,
containing a single set of chromosomes. Humans have 22 pairs of autosomal chromosomes and one pair of sex chromosomes (XX for females, XY for males).

3. Chromosomes are visualized through karyotyping, which arranges chromosomes based on size, banding patterns, and other characteristics. A karyotype provides information about
genetic disorders, chromosomal abnormalities, and gender by analyzing the number, size, and structure of chromosomes.

4. Heterochromatin is condensed chromatin that is transcriptionally inactive, while euchromatin is less condensed and involved in active transcription. Heterochromatin contains highly
repetitive sequences, whereas euchromatin contains genes that are actively transcribed.

5. Genes are coding regions of DNA responsible for producing proteins. They consist of exons (protein-coding sequences) and introns (non-coding sequences). Exons are spliced
together to form mature mRNA, which is then translated into proteins.

6. Nucleosides are bases bonded to a sugar, while nucleotides include a nucleoside and a phosphate group. In DNA structure, nucleotides make up the sugar-phosphate backbone
with bases attached and form the building blocks of the double helix.

7. Chargaff's rule states that in a DNA sample, the amount of Adenine equals the amount of Thymine, and the amount of Guanine equals the amount of Cytosine. This rule is essential
for understanding base composition and complementary base pairing in DNA.

8. DNA has a deoxyribose sugar, forms a double-stranded helix, and uses Thymine as one of the bases. RNA has a ribose sugar, is single-stranded, and uses Uracil instead of
Thymine. DNA is typically more stable than RNA due to its double-stranded structure.

9. The Central Dogma of molecular biology describes the ow of genetic information from DNA to RNA to proteins. DNA is transcribed into mRNA, which is then translated into
proteins. This process is essential for gene expression and protein synthesis.

10. Purines in DNA bases include Adenine and Guanine, while pyrimidines include Thymine and Cytosine. Purines have a double-ring
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