Genetics and Epigenetics Quiz

Molecular Genetics & Genetic Disorders

• The study covers Molecular Genetics and Genetic Disorders.
• Lecture objectives include explaining the molecular basis of genetics, describing different types of mutations and their impact on human health, introducing diagnostic techniques and molecular tools.
• Discussing the classification, examples, molecular pathogenesis, and inheritance patterns of genetic disorders is also a focus.
• Activities involve the foundation of Molecular Genetics, Molecular Diagnostics, Emerging Tools, Genetic Disorders (Chromosomal Disorders), and Genetic Disorders.
• Mendelian inheritance are listed as key topics to study.

Basic Foundation in Molecular Genetics

• The basic foundation covers Introduction to Genetics (terminology), DNA structure, Genome and Genes, Central dogma and gene expression, Coding & Non-coding regions, Mutation Overview, and Epigenetics concepts.

Key Genetic Terms & Definitions

• Genome: A complete set of genes.
• Gene: A unit of DNA for protein synthesis.
• Locus: A specific gene location on a chromosome.
• Allele: Variant forms of a gene.
• Genotype: Genetic makeup.
• Phenotype: Observable traits.
• Karyotype: A visual representation of a chromosome.

Define These Genetic Terms

• Polymorphism:
• Haploid and Diploid:
• Epigenetics:
• Penetrance:
• Expressivity:
• Noncoding DNA:
• Silent Mutation:
• Frameshift Mutation:
• Trinucleotide Repeat Expansion:
• Gene Heterogeneity:
• Pleiotropy:
• Anticipation:
• Mosaicism:
• Linkage Disequilibrium:
• Gene Therapy:

Structure of DNA

• DNA is a double helix with two strands wound around each other.
• DNA is made up of nucleotides: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G).
• Base pairing rules: A-T and C-G.
• DNA components include sugar (deoxyribose), phosphate, and base.

Organization of DNA

• Heterochromatin: Tightly packed, inactive regions of DNA.
• Euchromatin: Loosely packed, active regions of DNA.
• DNA wraps around protein to form nucleosomes.
• DNA is coiled into chromatin.
• Chromosomes form during cell division.

Central Dogma of Molecular Biology

• Flow of genetic information: DNA → RNA → Protein.
• Transcription: DNA to RNA.
• Translation: RNA to Protein.
• Enzymes involved: RNA Polymerase.
• Ribosomes.

Transcription-RNA Splicing-Translation

• DNA unwound by RNA polymerase.
• mRNA is synthesized using the DNA template strand.
• mRNA sequence is complementary to DNA (A pairs with U in RNA).
• RNA processing involves removing introns (non-coding regions), joining exons (coding regions), and forming mature mRNA for translation.
• Protein synthesis occurs when mRNA is read by ribosomes, tRNA brings amino acids, start codon is AUG (methionine), stop codons are UAA, UAG, UGA.

Genetic Code

• Triplet code: 3 nucleotides = 1 codon.
• Universal and degenerate codes: multiple codons for one amino acid.
• AUG is the methionine (start) codon.
• UAA, UAG, and UGA are stop codons.

Genome's "Dark Matter" = Noncoding Regions

• Long stretches of DNA, mainly devoted to regulation of gene expression.
• Noncoding regions can be considered as “architectural planning”, contrasting with “constructional materials”.
• LCR (locus control region) is a key element.

eg. LCR for HBB genes

• Locus Control Region (LCR) with the alpha globin locus and beta globin locus.
• LCR has conserved regions, initiating and termination sites, and an enhancer site.

Coding & Non-coding RNA

• mRNA (1,500-2,000 nt) is a coding RNA type.
• Long non-coding RNA.
• Small RNA includes snRNA, snoRNA, tRNA, miRNA, siRNA, piRNA, tsRNA.

Introduction to Mutation

• Permanent alterations in the DNA sequence.
• Mutations can be inherited or acquired.
• Mistakes in DNA replication, radiation, chemicals, and UV light can cause mutations.
• Mutations can occur in coding (exons), non-coding (introns), or regulatory regions, including splicing regions.
• Some are basis of genetic variability in some diseases.

Categories of Mutation

• Mutations can be grouped by scale (genome, chromosome, gene) and location (germline, somatic) and effects(silent, missense, nonsense, loss of function, gain of function).

Where is the location of the mutation? - Germ Line Vs Somatic Mutation

• Germline mutations occur in gametes, passed to offspring.
• Somatic mutations occur in non-germline cells, non-heritable.
• Examples: BRCA1/2, TP53

How much is the DNA's changed and lost?

• Genome mutation: loss or gain of chromosomes (monosomy, trisomy).
• Chromosomal mutation: rearranged genetic material, structural changes.
• Gene mutation: submicroscopic mutation; partial deletion of a gene or a single base change; point mutations, frameshift mutations, insertion or deletion, splicing mutations, termination mutations, trinucleotide repeat mutations.

Introduction to Mutation

• Types of mutations: silent, missense, nonsense, loss-of-function, gain-of-function mutations.

Epigenetics

• Heritable changes in gene expression without altering the DNA sequence.
• Key mechanisms:
  • DNA methylation: addition of methyl groups to DNA.
  • Histone modifications: altering histone proteins that DNA coils around.
  • Non-coding RNAs: regulating gene expression transcriptionally and post-transcriptionally.

Clinical Application of Epigenetics

• Cancer epigenetics: drugs targeting DNA methylation.
• Developmental disorders: role of imprinting.
• miRNA therapeutics: targeting miRNAs implicated in cancers.
• RNA Interference (RNAi): siRNA-based therapies.
• Epigenetic biomarkers for early disease detection..

Basic Foundation in Molecular Genetics (cont.)

• Introduction to methods in genetic disease diagnosis.
• Concept of karyotyping compared to molecular tests.
• Molecular applications of genetic tests.
• PCR basic concept & application.
• NGS basic concept & application.

Methods in the diagnosis of genetic disorders

• Genetic tests to detect genetic disorders: large abnormalities (chromosome level) to precise changes.

Methods For Mutation Analysis

• Detects large changes (chromosomes): cytogenetic techniques (karyotyping, FISH)
• Detects small changes (genes): PCR, Southern blot, qRT-PCR, digital PCR, Sanger sequencing, Pyrosequencing, NGS.

Karyotyping/Cytogenetic Analysis

• Method to analyze chromosomes.

Methods For DNA Analysis

• Traditional methods (Southern Blotting) vs newer/advanced methods (PCR-based techniques, Sanger Sequencing, NGS, epigenetic testing).

Principle of Polymerase Chain Reaction (PCR)

• Basic concepts: DNA denaturation, reannealing, synthesis,
• Specific DNA sequences can be copied and amplified.
• PCR tools.
• PCR reaction components.

Sanger Sequencing / Direct Nucleotide Sequencing

• Method to determine the order of nucleotides in a DNA sequence.

Next Generation Sequencing (NGS)

• Parallel sequencing of many DNA fragments.
• High throughput, speed, and scalability.