Genetic Code & Protein Synthesis

• DNA → RNA → Protein: essential for gene expression.

• Codons: Triplet nucleotides, 64 combinations for 20 amino acids, with redundancy.

Transcription & Translation

• Prokaryotic vs. Eukaryotic mechanisms:

  • Polycistronic mRNA in prokaryotes.

  • Histone unwrapping in eukaryotes.

• Splicing: removes introns; exons are expressed.

• Alternative splicing: allows one gene to produce multiple proteins.

DNA Mutations and Repair Mechanisms

• Types of damage: base modifications and strand breaks.

• Repair mechanisms:

  • High-fidelity: Homologous recombination.

  • Low-fidelity: Non-homologous end joining.

Mapping & Genetic Markers

• Mapping genes using recombination frequencies.

• Techniques: SNPs, VNTRs, linkage analysis.

• Uses: Identifying genetic diseases and studying inheritance.

DNA/RNA/Protein Analysis

• Blotting techniques:

  • Southern blot (DNA)

  • Northern blot (RNA)

  • Western blot (proteins).

• DNA sequencing methods: Sanger, pyrosequencing, NGS.

• Genetic mapping visual tools: Spectral karyotyping for chromosomal abnormalities.

Week 1 Summary of Key Points

1. Inheritance and Development

   • Early theories included concepts like the homunculus (miniature adult in sex cells) and spontaneous generation.

   • Theories evolved with the discovery of cellular structures and processes, leading to modern concepts of cell theory, genetics, and natural selection.

2. Evolution and Natural Selection

   • Darwin’s theory established the foundation of evolution by natural selection.

   • Adaptations and selection influence allele frequency and evolution within populations.

3. Discovery of Genetic Material

   • Mendel’s experiments on inheritance patterns in peas introduced the concept of dominant and recessive alleles.

   • Avery, MacLeod, and McCarty identified DNA as the carrier of genetic information.

4. DNA Structure and Function

   • Watson and Crick described DNA’s double-helix structure.

   • DNA and RNA are composed of nucleotides; DNA uses thymine while RNA uses uracil.

   • Base pairing (A-T, G-C) forms the DNA double helix, enabling replication and expression.

5. Chromosomes and DNA Replication

   • Eukaryotic and prokaryotic organisms differ in chromosome structure; eukaryotes use histones to package DNA.

   • DNA replication is semi-conservative, with mechanisms in place for proofreading and error correction.

Transcription in Prokaryotes and Eukaryotes

• Prokaryotic genes can be transcribed as polycistronic mRNAs (multiple genes per mRNA), while eukaryotic genes are monocistronic.

• Eukaryotes require transcription factors and histone modification to initiate transcription in a chromatin-based structure.

Genetic Code and Ribosomes

• Translation follows open reading frames (ORFs), ensuring proper amino acid sequences are produced.

• Mutations, like frame-shift mutations, can disrupt ORFs, altering protein function.

Gene Regulation Mechanisms

• Lac operon: The repressor binds the operator to block transcription in the absence of lactose. When lactose is present, it binds the repressor, enabling gene expression.

• Histone acetylation: Adds acetyl groups, loosening DNA-histone bonds, enhancing transcription.

• DNA methylation: Adds methyl groups to suppress transcription, often inherited during cell division.

Glossary

• mRNA (Messenger RNA): Transcribed RNA that carries coding information for protein synthesis.

• Splicing: Removal of introns from pre-mRNA; connects exons to form mature mRNA.

• Polycistronic mRNA: mRNA in prokaryotes that encodes multiple proteins.

• Tautomer: Alternate forms of nucleobases that can mispair, leading to mutation.

• Homologous Recombination: High-fidelity repair mechanism for double-strand breaks using a sister chromatid.

• Non-Homologous End Joining (NHEJ): Low-fidelity repair method for double-strand breaks without a template.

• SNP (Single Nucleotide Polymorphism): A single nucleotide variant; used in genetic mapping and association studies.

• Restriction Mapping: Technique to identify DNA fragments by cutting with restriction enzymes.

• Southern Blot: Technique to detect specific DNA sequences in DNA samples.

• PCR (Polymerase Chain Reaction): Method to amplify DNA segments for analysis.

• mRNA (Messenger RNA): The RNA copy of a gene that is translated into protein.

• Transcription Factors: Proteins that bind DNA to control transcription.

• Promoter: DNA region where transcription begins.

• Exon: Coding regions in a gene that remain in mRNA after splicing.

• Intron: Non-coding sequences removed by splicing.

• tRNA (Transfer RNA): Adapter molecules that translate mRNA codons into amino acids.

• Polycistronic mRNA: mRNA that encodes multiple proteins (common in prokaryotes).

• Lac Operon: Gene system in bacteria regulated by lactose presence.

• Chromatin Remodeling: Modifying histones to change DNA accessibility.

• Alternative Splicing: Process that enables a single gene to encode multiple proteins.

GEN2MHG WEEK 1-10 NOTES, Summary, glossary and flashcards

Summary of Key Points from Week 1 (Lessons 1 and 2)

1. Inheritance and Development

• Early theories included concepts like the homunculus (miniature adult in sex cells) and spontaneous generation.

• Theories evolved with the discovery of cellular structures and processes, leading to modern concepts of cell theory, genetics, and natural selection.

2. Evolution and Natural Selection

• Darwin's theory established the foundation of evolution by natural selection.

• Adaptations and selection influence allele frequency and evolution within populations.

3. Discovery of Genetic Material

• Mendel's experiments on inheritance patterns in peas introduced the concept of dominant and recessive alleles.

• Avery, MacLeod, and McCarty identified DNA as the carrier of genetic information.

4. DNA Structure and Function

• Watson and Crick described DNA’s double-helix structure.

• DNA and RNA are composed of nucleotides; DNA uses thymine while RNA uses uracil.

• Base pairing (A-T, G-C) forms the DNA double helix, enabling replication and expression.

5. Chromosomes and DNA Replication

• Eukaryotic and prokaryotic organisms differ in chromosome structure; eukaryotes use histones to package DNA.

• DNA replication is semi-conservative, with mechanisms in place for proofreading and error correction.

Detailed Notes

1. Inheritance and Development

   • Homunculus: Early belief that sex cells contained a mini adult.

   • Spontaneous Generation: Life from nonliving matter.

   • Fixity of Species: Species remain unchanged over time.

   • Lamarckism: Early theory on inherited characteristics (pre-epigenetics).

2. Evolution

   • Darwin and Wallace: Introduced natural selection.

   • Natural Selection: Traits that improve survival and reproduction are selected.

   • Adaptation: Populations develop traits that favor their environment.

3. Genetics and DNA

   • Mendel’s Principles: Dominant and recessive traits, segregation, and independent assortment.

   • Avery-MacLeod-McCarty Experiment: Proved DNA as genetic material.

4. DNA and RNA Structure

   • Nucleotide Components: Sugar, phosphate, and nitrogenous base.

   • Base Pairing: A-T, G-C in DNA; A-U in RNA.

   • Nucleic Acid Backbone: Alternating sugars and phosphates.

5. DNA Replication

   • Semi-Conservative Replication: Each new DNA molecule has one old and one new strand.

   • Proofreading: DNA polymerase corrects errors during replication.

Glossary

1. Homunculus: Early notion of a fully-formed mini-adult in reproductive cells.

2. Spontaneous Generation: The idea that life can arise from non-living matter.

3. Natural Selection: Process where organisms with favorable traits survive and reproduce.

4. Allele: Variant form of a gene.

5. DNA (Deoxyribonucleic Acid): Molecule carrying genetic instructions.

6. RNA (Ribonucleic Acid): Single-stranded nucleic acid, essential for protein synthesis.

7. Nucleotide: Basic building block of DNA and RNA.

8. Semi-Conservative Replication: DNA replication method where each strand serves as a template.

9. Transcription: Process of copying DNA to RNA.

10. Chromatin: DNA-protein complex in eukaryotic cells.

Flashcards

1. Q: What is the homunculus theory? A: The belief that sex cells contain a miniature adult.

2. Q: Who proposed the theory of natural selection? A: Charles Darwin and Alfred Russel Wallace.

3. Q: What are the components of a nucleotide? A: Sugar, phosphate group, and nitrogenous base.

4. Q: What base pairs are found in DNA? A: Adenine-Thymine (A-T) and Guanine-Cytosine (G-C).

5. Q: Define semi-conservative replication. A: A process where each new DNA double helix consists of one old strand and one new strand.

6. Q: What molecule was identified as the genetic material by Avery, MacLeod, and McCarty? A: DNA.

7. Q: What is chromatin? A: DNA wrapped around proteins in eukaryotic cells to form chromosomes.

8. Q: Which enzyme is responsible for proofreading during DNA replication? A: DNA polymerase.

9. Q: How does RNA differ from DNA? A: RNA is single-stranded and uses uracil instead of thymine.

10. Q: Describe natural selection. A: The process where organisms better adapted to their environment tend to survive and reproduce.

Let me know if you’d like more details in any of these sections!

WEEK 2 (L3-4)

Summary of Key Points from Week 2 (Lessons 3 and 4)

Lesson 3: Transcription and Translation

1. Genetic Material to Protein Synthesis

   • DNA is transcribed to mRNA, which carries genetic instructions to ribosomes where proteins are synthesized.

   • In prokaryotic transcription, RNA polymerase binds to promoter sequences to initiate transcription and synthesizes RNA until reaching a terminator sequence.

   • Eukaryotic transcription requires additional factors for initiation and involves processing steps like adding a 5' cap, poly-A tail, and splicing to produce mature mRNA.

2. Eukaryotic RNA Processing and Splicing

   • Exons represent coding sequences, while introns are non-coding and removed by the spliceosome during splicing.

   • Alternative splicing allows a single gene to produce multiple protein isoforms by including or excluding certain exons.

3. Genetic Code and Translation

   • The genetic code is a triplet codon system that translates mRNA to amino acids, with start and stop codons signaling the beginning and end of translation.

   • tRNA molecules match mRNA codons to amino acids with the help of aminoacyl tRNA synthetases.

   • Ribosomes assemble around mRNA to facilitate translation, which includes initiation, elongation, and termination.

4. Post-Translational Modifications

   • After translation, proteins undergo modifications like folding, phosphorylation, or glycosylation to become functional.

Lesson 4: Gene Regulation

1. Constitutive and Regulated Gene Expression

   • Some genes are expressed continuously (constitutive expression), while others are regulated by environmental signals.

   • The lac operon in bacteria exemplifies inducible expression, where genes are activated by the presence of lactose.

2. Regulation of Gene Expression in Eukaryotes

   • Eukaryotic gene regulation occurs at multiple levels, including transcription initiation, chromatin remodeling, and mRNA stability.

   • Chromatin remodeling (e.g., histone acetylation) and cytosine methylation impact gene accessibility and expression.

3. X Inactivation

   • In mammals, one of the X chromosomes in females is randomly inactivated, balancing gene dosage between sexes.

   • X inactivation can lead to mosaicism (e.g., in tortoiseshell cats) when heterozygous for X-linked traits.

4. Transcription Factors and Enhancers

   • Cis-acting elements (e.g., promoters) and trans-acting factors (e.g., transcription factors) control gene transcription.

   • Enhancers and silencers located at a distance can modulate expression levels by interacting with the transcription machinery.

5. Alternative Splicing and Protein Diversity

   • Alternative splicing allows one gene to produce proteins with different functions in various tissues, exemplified by the calcitonin gene.

6. Post-Translational Regulation

   • Proteins can be tagged for degradation through ubiquitination or modified in other ways to regulate their activity or lifespan.

Detailed Notes

1. Transcription in Prokaryotes and Eukaryotes

   • Prokaryotic genes can be transcribed as polycistronic mRNAs (multiple genes per mRNA), while eukaryotic genes are monocistronic.

   • Eukaryotes require transcription factors and histone modification to initiate transcription in a chromatin-based structure.

2. Genetic Code and Ribosomes

   • Translation follows open reading frames (ORFs), ensuring proper amino acid sequences are produced.

   • Mutations, like frame-shift mutations, can disrupt ORFs, altering protein function.

3. Gene Regulation Mechanisms

   • Lac operon: The repressor binds the operator to block transcription in the absence of lactose. When lactose is present, it binds the repressor, enabling gene expression.

   • Histone acetylation: Adds acetyl groups, loosening DNA-histone bonds, enhancing transcription.

   • DNA methylation: Adds methyl groups to suppress transcription, often inherited during cell division.

Glossary

1. mRNA (Messenger RNA): The RNA copy of a gene that is translated into protein.

2. Transcription Factors: Proteins that bind DNA to control transcription.

3. Promoter: DNA region where transcription begins.

4. Exon: Coding regions in a gene that remain in mRNA after splicing.

5. Intron: Non-coding sequences removed by splicing.

6. tRNA (Transfer RNA): Adapter molecules that translate mRNA codons into amino acids.

7. Polycistronic mRNA: mRNA that encodes multiple proteins (common in prokaryotes).

8. Lac Operon: Gene system in bacteria regulated by lactose presence.

9. Chromatin Remodeling: Modifying histones to change DNA accessibility.

10. Alternative Splicing: Process that enables a single gene to encode multiple proteins.

Flashcards

1. Q: What is the function of mRNA? A: To carry genetic information from DNA to ribosomes for protein synthesis.

2. Q: What are introns and exons? A: Introns are non-coding regions removed during splicing, while exons are coding regions included in the final mRNA.

3. Q: Describe the lac operon. A: A bacterial gene system that is activated by lactose, enabling transcription of lactose-metabolizing enzymes.

4. Q: What role do transcription factors play in eukaryotic transcription? A: They help initiate transcription by binding to promoters and recruiting RNA polymerase.

5. Q: Define alternative splicing. A: A process where pre-mRNA can be spliced in multiple ways, resulting in different proteins from a single gene.

6. Q: How does histone acetylation affect gene expression? A: It loosens DNA from histones, making it more accessible for transcription.

7. Q: Explain the function of tRNA in translation. A: tRNA carries amino acids to the ribosome, matching its anticodon with the mRNA codon to add amino acids to the growing protein chain.

8. Q: What is X inactivation? A: The process where one X chromosome in females is randomly silenced to balance gene expression with males.

Summary of Key Points from Week 3 (Lessons 5 and 6)

Lesson 5: DNA Damage and Repair

1. Types of DNA Damage and Their Causes

   • Tautomeric Shifts: Purines and pyrimidines can adopt alternative forms (tautomers), leading to incorrect base pairing.

   • Mutagens: Include reactive oxygen species (ROS), radiation (UV causing thymidine dimers), and chemicals like base analogues.

   • Spontaneous Changes: Deamination (loss of amino group) and depurination (loss of base) can occur, potentially causing mutations.

2. DNA Repair Mechanisms

   • Single-Strand Repair: Uses the undamaged complementary strand to restore the original sequence accurately.

   • Double-Strand Repair:

     • Homologous Recombination: High-fidelity repair using a sister chromatid as a template.

     • Non-Homologous End Joining (NHEJ): Error-prone method, often causing mutations, by directly ligating ends without a template.

3. Consequences of DNA Damage and Mutations

   • Germline vs. Somatic Mutations: Germline mutations are heritable, while somatic mutations affect only the individual.

   • Types of Mutations: Silent, missense, nonsense, and frameshift mutations can alter protein functionality.

   • Loss and Gain of Function: Loss-of-function mutations reduce gene activity, while gain-of-function mutations enhance or create new activity.

Lesson 6: Recombinant DNA Technology, PCR, and CRISPR

1. Recombinant DNA Technology

   • Restriction Enzymes: Cut DNA at specific sequences, creating "sticky" or "blunt" ends, allowing targeted DNA fragment insertion.

   • Plasmids as Vectors: Small, circular DNA used to amplify or express genes within bacteria.

   • Molecular Cloning: DNA fragments are inserted into plasmids, transformed into bacteria, and selected for by antibiotic resistance.

2. Polymerase Chain Reaction (PCR)

   • Steps: Denaturation, annealing of primers, and extension to amplify DNA.

   • Applications: Detects specific DNA sequences, quantifies DNA, and can introduce mutations.

   • RT-PCR: Converts mRNA into cDNA for amplification, useful for studying gene expression.

3. Gene Silencing and Editing

   • RNA Interference (RNAi): siRNAs bind to complementary mRNA, targeting it for degradation and reducing gene expression.

   • CRISPR/Cas9: Uses guide RNA to direct Cas9 to specific DNA sites, creating double-strand breaks for targeted editing.

Detailed Notes

1. DNA Damage Mechanisms

   • Radiation: UV radiation causes thymine dimers; X-rays cause double-strand breaks.

   • Chemical Mutagens: Include base analogues, alkylating agents, and intercalating agents, leading to mispairing or strand separation.

2. High-Fidelity DNA Repair Mechanisms

   • Base Excision Repair: Removes damaged bases and fills gaps with correct nucleotides.

   • Nucleotide Excision Repair: Excises bulky DNA lesions and restores correct sequence using the undamaged strand.

3. Polymerase Chain Reaction (PCR) Enhancements

   • Thermo-stable Polymerase: Taq polymerase, from Thermus aquaticus, withstands high denaturation temperatures.

   • Quantitative PCR (qPCR): Uses fluorescent dyes to measure DNA quantity, assessing initial template concentration.

4. CRISPR/Cas9 and Gene Editing

   • Guide RNA (gRNA): Directs Cas9 to the target DNA sequence.

   • Repair Pathways: NHEJ introduces insertions/deletions; homologous recombination can add specific sequences.

Glossary

1. Tautomer: Alternate form of a nucleotide base that can lead to incorrect base pairing.

2. Reactive Oxygen Species (ROS): By-products of cellular metabolism that can damage DNA.

3. Homologous Recombination: High-fidelity repair mechanism using a homologous sequence as a template.

4. Non-Homologous End Joining (NHEJ): Error-prone repair method for double-strand breaks.

5. Restriction Enzyme: Enzyme that cuts DNA at specific recognition sites.

6. Plasmid: Small, circular DNA molecule used as a vector in gene cloning.

7. PCR (Polymerase Chain Reaction): Technique to amplify specific DNA sequences.

8. RNA Interference (RNAi): Gene silencing technique that degrades target mRNA.

9. CRISPR/Cas9: Gene-editing technology using RNA-guided DNA cleavage.

10. Loss-of-Function Mutation: Mutation that reduces or eliminates gene activity.

Flashcards

1. Q: What causes thymine dimers in DNA? A: UV radiation.

2. Q: What is the purpose of homologous recombination in DNA repair? A: To repair double-strand breaks accurately using a sister chromatid as a template.

3. Q: How does a frameshift mutation affect a protein? A: Alters the reading frame, usually resulting in a nonfunctional protein.

4. Q: What role do plasmids play in molecular cloning? A: They act as vectors to insert and amplify DNA in bacteria.

5. Q: What is the main function of Taq polymerase in PCR? A: To synthesize DNA at high temperatures during PCR cycles.

6. Q: Describe the role of siRNA in RNA interference (RNAi). A: siRNA guides the RNA-induced silencing complex to degrade specific mRNA, reducing gene expression.

7. Q: What is the function of the guide RNA in CRISPR/Cas9? A: It directs Cas9 to a specific DNA sequence for precise cutting.

8. Q: Define a gain-of-function mutation. A: A mutation that enhances or creates a new function in the protein product.

Summary of Key Points from Week 4 (Lessons 7 and 8)

Lesson 7: DNA, RNA, and Protein Characterization

1. DNA Sequencing Methods

   • Sanger Sequencing: Uses dideoxynucleotides (ddNTPs) that terminate DNA extension. Each ddNTP is fluorescently labeled, allowing sequence determination by fragment length.

   • Next-Generation Sequencing (NGS): Processes multiple DNA fragments simultaneously, lowering costs and increasing speed.

   • Pyrosequencing: Detects nucleotide incorporation by light emission as bases are added, enabling fast sequencing.

2. Sequencing Advances

   • Sanger sequencing has given way to automated and massively parallel sequencing, making it feasible to sequence large genomes rapidly and cost-effectively.

   • The number of sequenced genomes has grown significantly, facilitating personalized genomics.

3. Blotting Techniques

   • Southern Blot: Used to detect specific DNA sequences.

   • Northern Blot: Detects RNA sequences, allowing analysis of gene expression.

   • Western Blot: Identifies specific proteins using antibodies.

Lesson 8: Genetic Mapping and GWAS

1. Linkage and Genetic Mapping

   • Linkage Analysis: Uses markers like microsatellites (STRs) and SNPs to locate genes related to specific traits or diseases by tracking recombination events.

   • Recombination Hotspots: Certain genome regions recombine more frequently, impacting map distances between genes.

2. Genome-Wide Association Studies (GWAS)

   • Purpose: Identifies genetic variants associated with diseases or traits by comparing SNP frequencies across populations.

   • Strengths and Limitations: GWAS is suited for common, polygenic traits but may overlook rare variants with large effects.

3. Types of Genetic Markers

   • STRs (Short Tandem Repeats): Repeated DNA sequences used for fine mapping.

   • SNPs (Single Nucleotide Polymorphisms): Single base changes, common and useful for high-resolution mapping and genotyping.

Detailed Notes

1. Sanger Sequencing and Advances

   • Dideoxynucleotides terminate the DNA chain when incorporated, allowing sequence readout by electrophoresis.

   • NGS and pyrosequencing significantly improve throughput by sequencing many DNA fragments simultaneously.

2. Blotting Techniques in DNA/RNA/Protein Analysis

   • Southern Blot: Identifies DNA sequences by hybridization after gel electrophoresis.

   • Northern Blot: Measures RNA levels, reflecting gene expression.

   • Western Blot: Detects proteins via antibody binding, used in protein characterization.

3. Genetic Mapping Markers and Recombination

   • Microsatellites and SNPs: Essential markers in genetic mapping, providing insights into the genomic loci associated with inherited traits.

   • Recombination Mapping: Tracks genetic markers in pedigrees, inferring distances between loci based on recombination rates.

4. GWAS Approach

   • Sample Size: Large cohorts and targeted SNPs improve association strength, identifying variants that contribute to complex traits.

   • Genomic Regions: GWAS highlights potential disease-related areas but may require further validation for clinical relevance.

Glossary

1. Sanger Sequencing: Method using ddNTPs for DNA chain termination to determine sequence.

2. Next-Generation Sequencing (NGS): High-throughput sequencing for large-scale DNA analysis.

3. Pyrosequencing: Sequencing method that emits light upon nucleotide addition.

4. Southern Blot: Technique to detect specific DNA sequences.

5. GWAS (Genome-Wide Association Study): Examines SNPs across genomes to identify trait-associated loci.

6. Microsatellites: Short, repetitive DNA sequences used in linkage analysis.

7. Single Nucleotide Polymorphism (SNP): A one-base variation in DNA, often used in genotyping.

8. Linkage Analysis: Maps genes by observing recombination between markers.

9. Recombination Hotspot: Regions with high recombination frequency.

10. LOD Score: Logarithm of odds, quantifying linkage likelihood between genes.

Flashcards

1. Q: What is the purpose of dideoxynucleotides in Sanger sequencing? A: They terminate DNA extension, allowing determination of the sequence by fragment length.

2. Q: What does Southern blotting detect? A: Specific DNA sequences.

3. Q: How does pyrosequencing detect DNA bases? A: By emitting light upon nucleotide incorporation.

4. Q: Define Genome-Wide Association Study (GWAS). A: A study that scans SNPs across the genome to find associations with traits or diseases.

5. Q: What role do SNPs play in genetic mapping? A: SNPs serve as markers for identifying genetic variations associated with specific traits.

6. Q: What is the function of Western blotting? A: To detect specific proteins using antibodies.

7. Q: Describe a recombination hotspot. A: A genomic region with increased recombination frequency, impacting gene mapping.

8. Q: What does a high LOD score indicate in linkage analysis? A: A high likelihood of linkage between two loci.

Summary of Key Points from Week 5 (Lessons 9 and 10)

Lesson 9: Gene Therapy Approaches

1. Gene Therapy Basics

   • Gene therapy introduces therapeutic genes into cells to treat genetic disorders.

   • Requires identification of the causative gene and accessibility to affected cells.

2. Gene Therapy Delivery Vectors

   • Viral Vectors: Commonly use viruses (e.g., adenovirus, retrovirus) to deliver genetic material, though they pose risks of immune response and integration issues.

   • Non-Viral Vectors: Lipid nanoparticles or chemical carriers used to reduce immune response risks.

3. Gene Therapy Case Studies

   • ADA-SCID: Patients with immune deficiency successfully treated with gene therapy targeting the IL2-Rγ gene.

   • OTC Deficiency: Fatal immune response in one case highlights the risks of viral delivery.

   • X-SCID: Retroviral vector caused leukemia due to insertion near proto-oncogenes, showing risks associated with insertional mutagenesis.

4. Gene Editing with CRISPR-Cas9

   • CRISPR-Cas9: Uses guide RNA to direct Cas9 to specific DNA sites, allowing precise gene editing.

   • Applications: Beta-thalassemia, lung cancer, and other conditions are undergoing trials.

Lesson 10: Personalized Medicine and Pharmacogenomics

1. Personalized Medicine

   • Tailors treatments based on individual molecular data to improve efficacy and minimize side effects.

   • Pharmacogenomics studies how genetic variations affect drug metabolism, enabling optimized dosage.

2. Targeted Drug Therapy

   • Herceptin for HER-2 Positive Cancers: Targeted drugs are designed for genetic profiles, such as HER-2 amplification in breast cancer.

   • Immunotherapy: Techniques like adoptive cell transfer (ACT) and CAR T-cell therapy enhance the patient’s immune system to target cancer cells.

3. Challenges in Personalized Medicine

   • Data Privacy: Managing and securing patient data.

   • Medical Training: Requires specialized knowledge for healthcare providers to interpret genetic data.

   • Technical and Ethical Issues: Handling large data volumes and ensuring patient rights.

Detailed Notes

1. Gene Therapy Vector Types

   • Adenovirus Vectors: High transduction efficiency but can provoke strong immune responses.

   • Retrovirus Vectors: Integrate into the host genome but pose risks of insertional mutagenesis, potentially activating oncogenes.

2. CRISPR-Cas9 in Gene Therapy

   • Mechanism: Guide RNA targets Cas9 to cut specific DNA sequences, enabling corrections or disruptions.

   • Advantages: Allows in vivo gene editing, creating potential for treating conditions without needing ex vivo modifications.

3. Pharmacogenomics and Drug Metabolism

   • CYP450 Enzymes: Variations in genes like CYP2D6 affect metabolism of drugs such as nortriptyline, influencing therapeutic response and risk of adverse effects.

4. Immunotherapy Techniques

   • Adoptive Cell Transfer (ACT): Extracts, expands, and reinfuses a patient’s tumor-infiltrating lymphocytes.

   • CAR T-Cells: Engineered T-cells with modified receptors to recognize and target specific cancer antigens.

Glossary

1. Gene Therapy: Technique to treat genetic disorders by inserting therapeutic genes.

2. Viral Vector: Virus-based carrier used to deliver genes into cells.

3. CRISPR-Cas9: Gene editing technology using guide RNA to target Cas9 enzyme to specific DNA sequences.

4. Pharmacogenomics: Study of how genetics affect drug metabolism and response.

5. Herceptin: Targeted drug for HER-2 positive breast cancer.

6. Adoptive Cell Transfer (ACT): Immunotherapy where a patient’s own immune cells are expanded and reinfused.

7. CAR T-Cell Therapy: Engineered T-cells with chimeric antigen receptors for targeted cancer treatment.

8. Insertional Mutagenesis: Gene disruption caused by viral vector integration near oncogenes.

9. Data Privacy: Protection of patient information in personalized medicine.

10. Cytochrome P450 (CYP450): Enzyme family involved in drug metabolism, impacted by genetic variations.

Flashcards

1. Q: What is the main goal of gene therapy? A: To treat genetic disorders by introducing therapeutic genes into patient cells.

2. Q: Name a risk associated with retroviral gene therapy vectors. A: Insertional mutagenesis, which can activate oncogenes and lead to cancer.

3. Q: How does CRISPR-Cas9 achieve precise gene editing? A: By using guide RNA to direct the Cas9 enzyme to specific DNA sequences.

4. Q: What is pharmacogenomics? A: The study of how genetic differences influence drug responses.

5. Q: What type of cancer is Herceptin used to treat? A: HER-2 positive breast cancer.

6. Q: What is Adoptive Cell Transfer (ACT) in immunotherapy? A: A method that expands a patient’s tumor-infiltrating lymphocytes to enhance immune response against cancer.

7. Q: Describe CAR T-cell therapy. A: Engineered T-cells are modified to target specific cancer antigens.

8. Q: What challenge does personalized medicine face with patient data? A: Ensuring data privacy and managing access rights.

Summary of Key Points from Week 6 (Lessons 11 and 12)

Lesson 11: DNA Forensics

1. DNA Profiling Techniques

   • DNA profiles can be generated using biological samples like saliva, blood, and other sources of cells.

   • VNTR Profiling: Uses Variable Number Tandem Repeats (VNTRs) in non-coding regions to identify individuals. VNTR sequences vary between individuals, providing unique patterns when analyzed across multiple loci.

   • STR Profiling: Short Tandem Repeats (STRs) are shorter sequences (2–9 base pairs) amplified via PCR and analyzed for their allele pattern. STR profiling is commonly used in forensic databases like CODIS (U.S.), which relies on 20 STR loci.

2. STR Analysis and Interpretation

   • STR profiles are analyzed by identifying allele patterns at multiple loci. Homozygous alleles show single peaks, and heterozygous alleles show double peaks on electropherograms.

   • Profile Probability: The probability of a random match decreases as more loci are analyzed. Using the product rule, allele frequencies are multiplied across loci to estimate profile uniqueness.

3. DNA Phenotyping

   • DNA phenotyping uses specific genetic markers to predict physical traits (e.g., eye, hair, and skin color) and ancestry, providing potential leads in forensic cases.

Lesson 12: Mitochondrial Disease and Therapy

1. Mitochondrial Function and Genome

   • Mitochondria generate energy via aerobic respiration, containing their own circular genome (mtDNA) with 37 essential genes.

   • mtDNA is maternally inherited, lacks histones, has limited repair mechanisms, and each cell contains multiple mitochondria with multiple copies of mtDNA.

2. mtDNA Mutations and Diseases

   • mtDNA is prone to mutations, often due to ROS from the electron transport chain. Mutations accumulate with cell divisions, leading to a mix of mutant and wild-type mtDNA (heteroplasmy).

   • Mitochondrial Diseases: Caused by high levels of mtDNA mutations, these diseases affect multiple organs, particularly brain and muscle tissue. Common symptoms include ataxia, dystonia, and myoclonic epilepsy.

3. Mitochondrial Replacement Therapy (MRT)

   • MRT, or “Three-Parent IVF,” replaces faulty mtDNA in embryos by transferring the nuclear DNA of the intended parents into a donor egg with healthy mitochondria.

   • Challenges of MRT include the potential incomplete removal of mutant mtDNA and ethical considerations related to embryo manipulation.

Detailed Notes

1. VNTR and STR Profiling in DNA Forensics

   • VNTRs: Longer, highly variable sequences ideal for identification but require more DNA and are less stable over time.

   • STRs: Preferred for forensics due to short sequence lengths, which are easier to amplify from degraded samples. Fluorescently tagged PCR primers assist in STR analysis, visualizing alleles by size on an electropherogram.

2. DNA Profiling Applications and Issues

   • Applications: Criminal identification, familial relationships, missing persons cases.

   • Challenges: Mixed or degraded samples, contamination, and partial profiles can complicate analysis.

3. Mitochondrial Genome Features and Mutation Accumulation

   • mtDNA accumulates mutations over time, especially in non-dividing cells like myocytes. Each daughter cell inherits a mix of mutant and wild-type mtDNA.

4. MRT Procedure and Limitations

   • MRT involves transferring parental nuclear DNA into a donor’s egg with healthy mitochondria. Despite advances, MRT may leave some mutant mtDNA in the embryo, posing risks for mitochondrial disease recurrence.

Glossary

1. VNTR (Variable Number Tandem Repeat): Non-coding DNA sequence with repeating units that vary among individuals.

2. STR (Short Tandem Repeat): Short DNA sequence repeated in tandem, commonly used in forensic profiling.

3. Profile Probability: Statistical probability of a DNA profile occurring in the general population.

4. DNA Phenotyping: Analysis of genetic markers to predict physical characteristics and ancestry.

5. Heteroplasmy: Presence of both normal and mutant mtDNA within a single cell.

6. Mitochondrial Replacement Therapy (MRT): Technique replacing defective mtDNA with donor mtDNA in embryos.

7. Electropherogram: A graph showing DNA fragments' size and intensity, used to interpret STR profiles.

Flashcards

1. Q: What is the primary difference between VNTR and STR profiling? A: VNTRs are longer sequences ideal for unique profiling, while STRs are shorter and preferred in forensics due to easier amplification.

2. Q: How is a DNA profile probability calculated? A: By multiplying allele frequencies at each locus, giving a unique probability for a specific DNA profile.

3. Q: What does DNA phenotyping reveal? A: Physical characteristics and ancestry information based on genetic markers.

4. Q: Why is mtDNA more prone to mutation? A: Lack of histones and limited DNA repair mechanisms make mtDNA susceptible to damage, especially from ROS.

5. Q: How does mitochondrial replacement therapy (MRT) work? A: It replaces defective mtDNA in embryos by transferring parental nuclear DNA into a donor egg with healthy mitochondria.

6. Q: Define heteroplasmy. A: The coexistence of both normal and mutant mtDNA in a single cell.

7. Q: What challenges are faced in DNA profiling of forensic samples? A: Issues include mixed or degraded samples, contamination, and partial DNA profiles.

Summary of Key Points from Week 7 (Lessons 13 and 14)

Lesson 13: Origins of Life and Early Evolution

1. RNA World Hypothesis

   • Life may have started with RNA, a molecule that can both store genetic information and catalyze reactions. RNA-based life could have existed before DNA and proteins evolved.

   • Ribozymes: RNA molecules with enzymatic activity, possibly allowing self-replication in early life forms.

2. Transition to DNA and Cellular Life

   • DNA eventually replaced RNA as the primary genetic material because it is more stable. Protein enzymes evolved to synthesize DNA, which allowed for more complex life forms.

   • Compartmentalization: Early cells likely formed by enclosing biomolecules within membranes, creating a stable environment for biochemical processes.

3. Eukaryotic Evolution

   • Eukaryotes likely emerged through endosymbiosis, where ancestral cells absorbed other prokaryotic cells (e.g., mitochondria).

   • Organelles such as mitochondria, chloroplasts, and the nucleus contributed to eukaryotic complexity, enabling larger, multicellular organisms.

4. Multicellularity

   • Multicellularity evolved independently in plants, fungi, and animals, driven by cell adhesion, communication, and specialization.

   • In multicellular organisms, evolution acts on the entire organism rather than individual cells.

Lesson 14: Mammalian and Human Evolution

1. Evolution of Mammalian Traits

   • Placental Mammals: Early mammals evolved distinct traits such as lactation and reduction of egg yolk genes (e.g., vitellogenin genes became inactive).

   • Lactation Evolution: Casein genes evolved from duplication events, enabling mammals to nourish offspring with milk.

2. Ape-Human Divergence

   • Humans and chimps diverged from a common ancestor. While there is ~4% genetic difference, humans share more genetic similarities with chimps than with other apes.

3. FOXP2 Gene and Speech

   • The FOXP2 gene, linked to speech and language, has mutations in humans that are absent in other primates. FOXP2 mutations cause speech disorders, indicating its role in vocalization.

4. Neanderthals and Denisovans

   • Interbreeding: Neanderthal and Denisovan DNA persists in non-African humans, providing beneficial adaptations (e.g., immunity genes, high-altitude adaptations in Tibetans).

   • Genetic Legacy: Archaic human DNA has influenced traits such as skin color, hair, and immune response in modern humans.

5. Lactase Persistence and Human Variation

   • Lactase Persistence: Genetic mutations allow some populations to digest lactose in adulthood. This trait arose independently in various populations through convergent evolution.

Detailed Notes

1. RNA World and Early Life

   • Ribozymes: Capable of catalyzing reactions, supporting the idea that early life may have used RNA instead of DNA.

   • Nucleotide Formation: Ribonucleotides could form under prebiotic conditions, potentially driven by UV light energy.

2. Evolution of Eukaryotes and Organelles

   • Endosymbiosis: The engulfing of bacteria by ancestral cells led to mitochondria and chloroplasts, supporting complex cellular functions.

   • Cell Specialization: Multicellularity required mechanisms for cell adhesion, signaling, and differentiation.

3. Human Evolutionary Traits

   • FOXP2 and Speech: Humans' unique FOXP2 mutations relate to speech development, showing how genetic changes support complex communication.

   • Archaic Gene Retention: Neanderthal and Denisovan genes in modern humans provide traits like high-altitude adaptation (EPAS-1 variant in Tibetans).

4. Lactase Persistence and Adaptation

   • Populations with a history of dairy farming developed lactase persistence, allowing adults to digest lactose. Mutations in regulatory regions of the LCT gene enhance lactase expression.

Glossary

1. RNA World Hypothesis: Theory that life began with RNA, which could store information and catalyze reactions.

2. Ribozyme: RNA molecule with enzymatic activity, supporting self-replication in early life.

3. Endosymbiosis: Process by which eukaryotic cells acquired organelles (e.g., mitochondria) from engulfing prokaryotes.

4. FOXP2 Gene: A gene associated with speech development, with unique mutations in humans.

5. Lactase Persistence: The ability to digest lactose in adulthood due to mutations in the LCT gene enhancer.

6. Heteroplasmy: Presence of both normal and mutated mtDNA within cells.

7. Convergent Evolution: Independent evolution of similar traits in different populations (e.g., lactase persistence).

Flashcards

1. Q: What is the RNA World Hypothesis? A: The theory that early life was based on RNA, capable of storing genetic information and catalyzing reactions.

2. Q: How did endosymbiosis contribute to eukaryotic evolution? A: Eukaryotic cells acquired organelles like mitochondria through endosymbiosis, increasing cellular complexity.

3. Q: What is the role of the FOXP2 gene in humans? A: It is associated with speech development; mutations in FOXP2 can lead to speech disorders.

4. Q: Describe lactase persistence and its evolutionary significance. A: Lactase persistence allows adults to digest lactose; it evolved independently in dairy-farming populations.

5. Q: What is heteroplasmy? A: The presence of both normal and mutant mtDNA within a single cell, leading to mixed genetic outcomes.

6. Q: Explain the significance of Neanderthal and Denisovan DNA in modern humans. A: These archaic genes contribute to traits like immune response and high-altitude adaptation.

7. Q: What is convergent evolution? A: The independent evolution of similar traits in different populations, such as lactase persistence in various regions.

Summary of Key Points from Week 8 (Lessons 15 and 16)

Lesson 15: Aneuploidy and Chromosomal Abnormalities

1. Aneuploidy and Non-Disjunction

   • Aneuploidy occurs when there is an abnormal number of chromosomes due to non-disjunction during meiosis, resulting in gametes with extra or missing chromosomes.

   • Monosomy (loss of one chromosome) and trisomy (gain of one chromosome) are common forms, with severe consequences for development.

2. Autosomal Monosomy and Trisomy

   • Autosomal Monosomy: Lethal in humans as it causes a lack of essential gene dosage.

   • Autosomal Trisomy: Trisomy 21 (Down syndrome) is viable and leads to characteristic physical and mental traits. Trisomies 13 and 18 are usually lethal shortly after birth.

3. Sex Chromosome Abnormalities

   • Individuals can survive with abnormal numbers of sex chromosomes due to mechanisms like X-inactivation. Examples include:

     • Turner Syndrome (45, X): Only one X chromosome; associated with short stature and ovarian dysfunction.

     • Klinefelter Syndrome (47, XXY): Extra X in males, often leading to mild cognitive deficits and sterility.

4. Polyploidy and Its Mechanisms

   • Polyploidy (more than two sets of chromosomes) is rare in humans but common in plants and some animals. It can arise from errors in meiosis or fertilization.

   • Examples: Triploid and tetraploid organisms are usually sterile due to abnormal chromosome segregation during meiosis.

5. Structural Chromosomal Alterations

   • Deletions: Loss of a chromosomal segment (e.g., Cri du Chat syndrome).

   • Inversions: Reversed orientation of a chromosomal segment; often asymptomatic but can lead to abnormal gametes.

   • Translocations: Segmental exchange between chromosomes, which can lead to fertility issues and genetic disorders like familial Down syndrome.

Lesson 16: Genetic Disorders and Pedigree Analysis

1. Autosomal Recessive Disorders

   • Disorders such as oculocutaneous albinism (OCA) and cystic fibrosis (CF) follow an autosomal recessive inheritance pattern, where individuals with two mutated alleles are affected.

   • Cystic Fibrosis: Caused by mutations in the CFTR gene; affects lung and digestive function due to thick mucus buildup. Treatments include symptom management and specific drugs targeting CFTR mutations.

2. Pedigree Analysis for Inheritance Patterns

   • Pedigrees help determine if a disorder is autosomal recessive, autosomal dominant, or X-linked. Autosomal recessive traits often appear in siblings but not parents.

   • Genotype-Phenotype Relationship: In CF, severity depends on specific mutations in CFTR, with variations in protein function leading to different clinical outcomes.

3. Advances in Targeted Therapy for CF

   • Correctors and potentiators: Drugs developed to address specific CFTR mutations. For example, Ivacaftoris used for CFTR mutations that affect channel activity, improving lung function in certain patients.

4. Environmental and Genetic Modifiers

   • Variants in other genes and environmental factors can influence disease severity, particularly in CF. Lung infections exacerbate symptoms, and genetic modifiers affect pancreatic and respiratory health.

Detailed Notes

1. Aneuploidy and Its Consequences

   • Down Syndrome (Trisomy 21): Most common viable trisomy, with physical and developmental traits. Incidence increases with maternal age.

   • Sex Chromosome Abnormalities: Generally less severe due to mechanisms like X-inactivation, allowing survival despite extra sex chromosomes.

2. Polyploidy in Evolution and Agriculture

   • Polyploid plants (e.g., seedless fruits) are often sterile and propagated asexually. Polyploidy can lead to new species over evolutionary time, especially in plants.

3. Genetic Basis of Cystic Fibrosis

   • CFTR Mutations: The most common mutation, F508del, impairs protein folding, leading to severe symptoms. Other mutations (e.g., G551D) affect chloride channel function.

4. Pedigree Analysis Techniques

   • Autosomal Recessive Disorders: Typically appear in children with unaffected carrier parents. Analysis can identify carriers and predict offspring risks.

Glossary

1. Aneuploidy: Presence of an abnormal number of chromosomes due to errors in cell division.

2. Non-Disjunction: Failure of chromosomes to separate properly during meiosis, leading to aneuploidy.

3. Trisomy: Condition of having three copies of a chromosome (e.g., Trisomy 21 in Down syndrome).

4. Turner Syndrome: Monosomy X (45, X), characterized by short stature and ovarian dysfunction.

5. Polyploidy: Having more than two complete sets of chromosomes; common in plants.

6. CFTR (Cystic Fibrosis Transmembrane Conductance Regulator): Gene mutated in cystic fibrosis, causing defective chloride ion transport.

7. Corrector/Potentiator Drugs: Medications that enhance folding or channel activity of CFTR proteins in CF patients.

Flashcards

1. Q: What is aneuploidy, and what causes it? A: Aneuploidy is an abnormal chromosome number, often caused by non-disjunction during meiosis.

2. Q: What are common examples of trisomy in humans? A: Trisomy 21 (Down syndrome), Trisomy 13, and Trisomy 18.

3. Q: How does Turner syndrome arise? A: Turner syndrome results from having only one X chromosome (45, X) and causes developmental abnormalities in females.

4. Q: Describe the role of the CFTR gene in cystic fibrosis. A: CFTR encodes a chloride ion channel; mutations lead to thick mucus buildup in lungs and digestive issues.

5. Q: What are corrector and potentiator drugs? A: Correctors improve CFTR protein folding, and potentiators enhance channel function, used in targeted CF therapies.

6. Q: How can polyploidy contribute to speciation in plants? A: Polyploidy can create new plant species by increasing chromosome sets, often leading to sterility but allowing asexual propagation.

7. Q: What is the genetic basis of oculocutaneous albinism (OCA)? A: OCA is caused by autosomal recessive mutations in genes involved in melanin production, leading to lack of pigmentation.

Summary of Key Points from Week 9 (Lessons 17 and 18)

Lesson 17: Autosomal Dominant Disorders and Marfan Syndrome

1. Characteristics of Autosomal Dominant Inheritance

   • Autosomal dominant disorders affect both sexes and are passed down from one affected parent.

   • The risk of an affected parent passing the disorder to a child is 50%.

   • These disorders are relatively rare, especially when they involve severe phenotypes.

2. Mechanisms of Dominant Mutations

   • Gain-of-Function Mutations: Increase gene expression, alter timing, or create abnormal activity in new cell types.

   • Haploinsufficiency: Insufficient protein from a single wild-type allele causes a phenotype.

   • Dominant-Negative Effects: Mutant protein interferes with normal protein function, particularly if the protein forms multimers.

3. Marfan Syndrome

   • A connective tissue disorder affecting multiple organs, caused by mutations in the FBN1 gene (encoding fibrillin-1).

   • Common symptoms include aortic dilation, bone overgrowth, and eye issues like lens dislocation.

   • Mechanisms include haploinsufficiency (insufficient fibrillin-1) and dominant-negative effects (mutant monomers disrupt fibril structure).

   • Treatment focuses on managing symptoms, e.g., using beta-blockers and regular cardiovascular monitoring.

Lesson 18: Li-Fraumeni Syndrome and Non-Mendelian Inheritance

1. Li-Fraumeni Syndrome (LFS)

   • A cancer predisposition syndrome linked to mutations in the p53 tumor suppressor gene, following an autosomal dominant pattern.

   • p53 Function: A transcription factor that induces cell cycle arrest, DNA repair, or apoptosis in response to cellular stress.

   • Dominant-Negative Mutations: Mutant p53 monomers prevent normal p53 tetramers from functioning, leading to impaired tumor suppression.

   • Inheritance and Penetrance: Affected individuals inherit one defective p53 allele and have a high risk of early-onset cancers, but not all carriers develop cancer.

2. Non-Mendelian Inheritance Patterns

   • Incomplete Penetrance: Not all individuals with a mutation show symptoms, influenced by other genetic or environmental factors.

   • Anticipation: Some disorders worsen or appear earlier in successive generations.

   • Imprinting and X/Y-Linked Traits: Specific inheritance patterns deviate from classic Mendelian genetics, as seen in mitochondrial inheritance and X-linked traits.

3. Example of X-Linked Recessive Disorder: Duchenne Muscular Dystrophy (DMD)

   • Affects primarily males, as females are usually carriers with mild or no symptoms.

   • Caused by mutations in the DMD gene (encoding dystrophin), leading to progressive muscle weakness.

   • Exon-Skipping Treatments: Targeted therapies encourage skipping of specific exons to restore the reading frame and produce a functional protein.

Detailed Notes

1. Autosomal Dominant Disorders

   • Inheritance Patterns: An affected person has a 50% chance of passing the mutation to offspring, regardless of the child’s sex.

   • Mechanisms: Dominant mutations include gain-of-function, haploinsufficiency, and dominant-negative mutations that disrupt normal protein complexes.

2. Marfan Syndrome and Fibrillin-1

   • Fibrillin-1 mutations affect connective tissues by altering TGF-β signaling and compromising structural integrity.

   • Patients are managed through cardiovascular interventions, physical activity limitations, and regular imaging for aortic monitoring.

3. Li-Fraumeni Syndrome and p53 Mutation Effects

   • p53 functions as a tetramer, and dominant-negative mutations in one allele can disrupt the entire protein complex, significantly impacting tumor suppression.

   • LFS presents a unique cancer risk profile, including breast cancer, sarcomas, and other cancers at unusually young ages.

4. Duchenne Muscular Dystrophy (DMD)

   • Genetic Mechanism: Mutations disrupt dystrophin’s role in stabilizing muscle cell membranes, leading to muscle degeneration.

   • Treatment Strategies: Includes exon-skipping agents like Eteplirsen, which promote alternative splicing to restore partial dystrophin function.

Glossary

1. Autosomal Dominant Disorder: A genetic disorder passed down from one affected parent, with a 50% inheritance risk.

2. Gain-of-Function Mutation: Mutation that enhances or alters protein function, often causing abnormal activity.

3. Haploinsufficiency: Occurs when one functional copy of a gene does not produce enough protein for normal function.

4. Dominant-Negative Mutation: Mutant protein interferes with normal protein function, especially in multimeric proteins.

5. Marfan Syndrome: A connective tissue disorder associated with mutations in the FBN1 gene.

6. Fibrillin-1 (FBN1): Protein that forms structural fibrils in connective tissue and regulates TGF-β signaling.

7. Li-Fraumeni Syndrome: Cancer predisposition syndrome caused by mutations in the p53 tumor suppressor gene.

8. Duchenne Muscular Dystrophy (DMD): X-linked recessive disorder caused by mutations in the dystrophin gene, leading to muscle degeneration.

9. Exon Skipping: A therapeutic approach to restore the reading frame by removing specific exons in mutated genes.

10. Non-Mendelian Inheritance: Patterns of inheritance that do not follow Mendel’s laws, including traits with incomplete penetrance and anticipation.

Flashcards

1. Q: What is an autosomal dominant disorder? A: A disorder that affects individuals with one mutated allele, with a 50% chance of passing it to offspring.

2. Q: How does a gain-of-function mutation impact a protein? A: It enhances or alters the protein’s activity, potentially causing abnormal cellular effects.

3. Q: What is haploinsufficiency? A: A condition where a single functional allele does not produce enough protein for normal function.

4. Q: Describe the genetic basis of Marfan syndrome. A: Caused by mutations in the FBN1 gene, affecting connective tissues and TGF-β signaling.

5. Q: What is Li-Fraumeni syndrome? A: A cancer predisposition syndrome linked to mutations in the p53 tumor suppressor gene.

6. Q: Why are dominant-negative mutations particularly harmful in multimeric proteins? A: Mutant monomers disrupt the entire protein complex, impairing its function.

7. Q: What therapeutic approach is used for Duchenne muscular dystrophy (DMD)? A: Exon skipping, which removes specific exons to restore a functional protein.

8. Q: Define non-Mendelian inheritance. A: Inheritance patterns that deviate from classic Mendelian laws, including traits with incomplete penetrance and anticipation.

Summary of Key Points from Week 10 (Lessons 19 and 20)

Lesson 19: X-Linked Dominant Disorders and Fragile X Syndrome

1. Characteristics of X-Linked Dominant Inheritance

   • Affects both sexes but often shows milder symptoms in females due to X-inactivation.

   • Males with an affected X chromosome exhibit more severe symptoms, as they lack a second X to counterbalance the mutation.

   • If the father is affected, all daughters will inherit the disorder, but sons will not.

2. Fragile X Syndrome

   • Caused by mutations in the FMR1 gene, specifically by an expansion of CGG repeats.

   • Repeat Expansion and Symptoms: Fewer than 50 CGG repeats is normal; 50-200 is a premutation (often asymptomatic); over 200 repeats lead to Fragile X syndrome.

   • Symptoms: Intellectual disability, anxiety, seizures, distinctive facial features, and autism-like behaviors.

   • Anticipation: Repeats can expand in successive generations, increasing severity, particularly with maternal transmission.

   • Gene Silencing: Large repeat expansions lead to DNA methylation and silencing of the FMR1 gene, reducing FMRP protein levels.

3. Incomplete Dominance in Fragile X

   • Females with one affected allele generally show milder symptoms, due to random X-inactivation, which leaves some cells with a functional FMR1 gene.

Lesson 20: Epigenetics and Imprinting Disorders

1. Imprinting and Epigenetic Regulation

   • Imprinting involves parental-specific expression of certain genes, regulated by DNA methylation and histone modifications.

   • Example Disorders: Angelman and Prader-Willi syndromes are caused by loss of function of imprinted genes on chromosome 15, with phenotypic outcomes depending on whether the affected gene is maternally or paternally inherited.

2. Imprinting Disorders

   • Prader-Willi Syndrome: Caused by loss of paternal expression of the SNORD116 gene; symptoms include excessive appetite, hormonal issues, and intellectual disability.

   • Angelman Syndrome: Results from loss of maternal expression of UBE3A, leading to neurological issues, including intellectual disability and a distinct behavioral phenotype.

3. Gene-Environment Interactions and Epigenetic Modifications

   • Environmental exposures (e.g., diet, toxins) during pregnancy can modify DNA methylation patterns, impacting gene expression in offspring.

   • Example: In utero exposure to chemicals like bisphenol A (BPA) can reduce methylation and alter phenotypes.

4. Case Study in Gene-Environment Interaction: Phenylketonuria (PKU)

   • Cause: PKU is caused by mutations in the PAH gene, which normally metabolizes phenylalanine into tyrosine.

   • Symptoms: High phenylalanine levels lead to intellectual disability.

   • Treatment: A low-phenylalanine diet prevents the severe cognitive symptoms of PKU, highlighting the interaction between genetics and environment.

Detailed Notes

1. Fragile X Syndrome and Anticipation

   • Fragile X shows genetic anticipation, where the disorder’s severity can increase in each generation, especially when the mutation is maternally inherited.

   • CGG repeats trigger hypermethylation, silencing FMR1 and reducing levels of FMRP, an RNA-binding protein critical for neuron function.

2. Imprinting Mechanism and Disorders

   • Prader-Willi and Angelman Syndromes: Both arise from a cluster of imprinted genes on chromosome 15, but symptoms depend on whether the deletion or mutation is on the paternal or maternal chromosome.

   • Parental-Specific Expression: For some genes, only one allele (maternal or paternal) is active, while the other is silenced through methylation.

3. Gene-Environment Interactions

   • Epigenetic changes like DNA methylation can be influenced by environmental factors.

   • Transgenerational Epigenetics: In utero environmental effects may influence methylation and gene expression, but evidence for lasting inheritance across multiple generations in humans is limited.

4. PKU: Gene and Environmental Interaction

   • PKU demonstrates how diet can modify the phenotypic outcome of a genetic disorder. By restricting phenylalanine intake, cognitive deficits can be largely prevented.

Glossary

1. X-Linked Dominant Inheritance: A pattern where a mutation on the X chromosome causes a disorder that affects both sexes, with more severe symptoms in males.

2. Fragile X Syndrome: A disorder due to CGG repeat expansions in the FMR1 gene, leading to intellectual disability and other symptoms.

3. Anticipation: A phenomenon where genetic disorders worsen or appear earlier in successive generations, often linked to repeat expansions.

4. Imprinting: Parent-specific gene expression where only one allele is active, depending on its parental origin.

5. Prader-Willi Syndrome: Caused by a lack of paternal expression of SNORD116, resulting in excessive appetite, obesity, and developmental issues.

6. Angelman Syndrome: Caused by a lack of maternal expression of UBE3A, leading to neurological and behavioral symptoms.

7. Epigenetics: Study of changes in gene expression that do not involve alterations in the DNA sequence, often through DNA methylation and histone modification.

8. Phenylketonuria (PKU): A metabolic disorder caused by mutations in PAH, leading to phenylalanine buildup; treated with dietary management.

9. Methylation: Addition of a methyl group to DNA, often silencing gene expression, particularly in promoter regions.

10. Gene-Environment Interaction: The interplay between genetic predispositions and environmental factors in determining phenotype.

Flashcards

1. Q: What characterizes X-linked dominant inheritance? A: It affects both sexes, often with milder symptoms in females due to X-inactivation, and is fully passed from affected fathers to all daughters but not sons.

2. Q: What causes Fragile X syndrome? A: Expansions of CGG repeats in the FMR1 gene leading to hypermethylation and gene silencing.

3. Q: Define anticipation in genetics. A: A pattern where disorders worsen or appear earlier in each generation, commonly seen in repeat expansion disorders.

4. Q: What is imprinting? A: Parent-specific gene expression where only one allele (maternal or paternal) is active due to epigenetic silencing of the other.

5. Q: What distinguishes Prader-Willi from Angelman syndrome? A: Prader-Willi syndrome results from a loss of paternal expression of SNORD116, while Angelman syndrome results from a loss of maternal expression of UBE3A.

6. Q: What environmental factor impacts DNA methylation? A: Exposure to certain chemicals (e.g., BPA) during pregnancy can modify offspring’s DNA methylation patterns and phenotypes.

7. Q: How does a low-phenylalanine diet affect PKU patients? A: It prevents intellectual disability by reducing phenylalanine levels in the brain.

8. Q: What is the role of DNA methylation in gene expression? A: Methylation usually silences gene expression by preventing transcription factor binding in promoter regions.