BMS 532: Biochemistry of Genetics and DNA Structure Lecture Notes (PDF)

A Quick Introduction… BMS 532 BLOCK 3 LECTURE 1  A Few Key Scientists in the History of Genetics Avery, McLeod,...

A Quick Introduction… BMS 532 BLOCK 3 LECTURE 1  A Few Key Scientists in the History of Genetics Avery, McLeod, Rosalind Franklin Gregor Mendel Sutton and Boveri Hermann Joseph Muller Joachim Hammerling and McCarty X-ray diffraction Patterns of Chromosome X-ray induction of Genetic information is DNA is studies that Heredity in Pea Theory of Heredity mutations/Radiation located in the nucleus of responsible for demonstrated Plants Proposed causes genetic mutation the cell transformation structure of DNA 1865 1902 1930s-1940s 1944 as double helix 1927 1953 1941 1950 1952 1869 1915 1928 1931 Erwin Chargaff Hershey and Thomas Hunt Frederick Griffith Barbara McClintock Rules of base Chase Friedrich Miescher Morgan Bacterial Transposon association Radiolabeling Earliest Identification Confirmation of Transformation experiments in corn A:T and G:C of DNA of nucleic acids Chromosome Theory Transforming Genetic demonstrating (Nuclein) of Inheritance pathogenicity into recombination in corn Beadle and DNA as Drosophila nonpathogenic Corn Cytogenetics Tatum hereditary Experiments bacteria One Gene-One material Enzyme Hypothesis  A More Modern Brief History of Genetics: Providing A Little Relative Perspective Not every generation alive today has known of DNA since childhood ◦ Structure of DNA = 1953 (Watson and Crick using Franklin and Chargraff Data) ◦ Existence of mRNA = 1961 ◦ Genetic Code Deciphered = 1961 ◦ Recombinant DNA Technology = 1973 ◦ Sanger Sequencing = 1977 These are merely a snapshot of ◦ 1st Genome Sequenced = Bacteriophage some of the major moments in ◦ PCR Developed = 1983 Genetics ◦ Beginning of Human Genome Project = 1990 ◦ Genetic Engineering in Corn Approved by FDA = 1995 How did each of these ◦ 1st Human Chromosome (22) Sequenced = 1999 discoveries impact the field? ◦ Human Genome Reference Sequence Completed (Human Genome Project) = 2003 How did each of these enhance ◦ Cancer Genome Atlas Initiated = 2006 our understanding of human ◦ Full Sequence of a Child’s Genome used clinically for diagnosis of a new disease = 2009 health? ◦ Noninvasive Prenatal Testing becomes commercially available for clinical application = 2011-2012 ◦ Genome projects that focus on sequencing thousands of humans are initiated = 2012 What do you think is the most ◦ Cost of sequencing a whole genome drops to $1000.00 = 2014 important discovery/event in ◦ TCGA publishes Pan-Cancer Atlas = 2018 Molecular Genetics for your ◦ Clinical Application for CRISPR-Cas in Sickle Cell Anemia = 2020 lifetime? ◦ Increased accessibility of whole genome sequencing in the diagnosis of rare diseases = 2022 ◦ Advances in whole genome sequencing in diagnostics = ONGOING! Objectives 1. Define the following terms using both technical and working definitions: Molecular Genetics, Genome, Transcriptome, Proteome, Polypeptide, Metabolome, Genotype, and Phenotype 2. Summarize the central dogma of molecular genetics and explain the conceptual hierarchy of molecular genetics in terms of how and when genetic information is observed phenotypically 3. Explain the relationship between DNA, RNA, and protein in terms of how each influences and interacts with one another 4. Explain how molecular analyses contribute to our understanding of biological function with emphasis on “omics” and their role in diagnostics  Critical Introductory Terminology Working Definitions for terms you potentially use every day: Key Foundational Terms for the Block: What is DNA? DNA, RNA, Protein What is a Gene? Gene, Genome, Genotype What is a Genome? Chromosome, Chromatin, Chromatid Transcriptome, Proteome, Metabolome Phenotype LO1, LO2  The Central Dogma of Molecular Genetics DNA is transcribed into RNA which is Translated into Protein Molecular Expression of Genes Determines an Organism’s Traits Reverse Transcription LO1, LO2, LO3  The Wider World of -Omics Genomics only provides part of the picture ◦ Transcriptomics tells you what genes are active ◦ Proteomics = study of protein complement of the cell/organism ◦ Protein Equivalent ◦ Can lead to a better understanding of functional consequences ◦ Metabolomics refers to the functional activity of gene products related with metabolism (biochemical properties of gene products) Having a particular gene or DNA sequence does NOT guarantee that you will have the corresponding phenotype to the greatest degree of expression ◦ i.e. Variable expression and penetrance LO1, LO3, LO4 Steuer et al 2019  Modern Molecular Genetics Applications for Genetics in a wide range of fields including agriculture, biotechnology, fuels, and more Application of Genetics to Human Health and Disease ◦ Preimplantation Genetic Diagnosis in in vitro fertilization ◦ Risk Assessment for probability of developing a given condition ◦ Genome Sequencing for early detection and diagnosis ◦ Identification of polymorphisms that are naturally occurring variation vs. associated with pathogenicity ◦ Pharmacogenetics: Drug Development and Improvement LO4 Biochemistry of Genetics and DNA Structure BMS 532 BLOCK 2 LECTURE 1 CONTINUED  Objectives 5. List the criteria for genetic information and explain why genetic material must meet this criteria 6. Describe the structure of DNA including base-pairing, directionality, and complementarity based on the Watson-Crick Model 7. Explain the forces involved in generating the stability of the double-stranded DNA molecule and how this compares to single-stranded alternatives 8. Summarize the 3 forms of DNA discussed (B, A, and Z) and explain the implications of each form on function 9. Explain how DNA sequences correlate with DNA structure/form and stability of the overall molecule 10. Compare and Contrast double-stranded and single-stranded DNA in terms of their stability and replication 11. Define the term C-value and explain the C-value paradox 12. Assess the consequences for changes (typical variation and mutation) in DNA sequence on DNA structure, mRNA product, protein product, and overall gene function and link these changes to human variation or disease** **This is a major aim and theme for the entire block  The 4 Criteria of Genetic Information Contain Information ◦ Must contain the information necessary to construct an organism in its entirety Transmissibility ◦ Must be passed from parents to offspring (cell to daughter cells) Replication ◦ Must be capable of being copied or reproduced to be passed from parents to offspring (cell to daughter cells) Variation ◦ Must be capable of containing variable information that accounts for the diversity of observable differences within a species LO5  Structure of DNA Tetranucleotide Sequence Deoxyribose sugar because missing 2’ hydroxyl of ribose sugar 3D structure of DNA involves 2 strands antiparallel to one another with planar base-pairs that exist nearly perpendicular to the helical axis ◦ Sequences are said to have directionality due to binding between 3’ and 5’ carbons of the LO6 sugar backbone  DNA Stability Stability conferred by 3 major forces ◦ Number of hydrogen bonds ◦ Hydrophobic interactions ◦ Van der Waals forces acting among stacking bases Although the hydrogen bonds are weak individually, collectively in combination with additional factors they serve to generate a VERY stable molecule Aromatic base-stacking contributes to the stability ◦ Explains the differences in melting temperatures for DNA and RNA DNA is so stable it can be handled in the lab at room temperature for short periods of time LO7, LO9 Aromatic basically means :  Stability with Ability to Change DNA must be stable to ensure that the encoded information is maintained for function As indicated in the criteria for genetic information, it must also have the potential for change The ability to change through mutation increases genetic variation ◦ Variation accounts for phenotypic diversity AND is essential for evolution of a population/species LO6, LO7  Hydrogen Bonding Base pairs are associated by weak bonds: Hydrogen Bonds A to T pairing = 2 bonds G to C pairing = 3 bonds As predicted, DNA denaturation experiments have demonstrated that DNA containing a higher content of G-C base pairs is more stable (requires higher temperatures for separation) LO6, LO7, LO9 LO6, LO7, LO9 Chargaff/Watson-Crick Base-Pairing O N T C N O G N N A N O N O N LO6, LO8 Major and Alternative Forms of DNA B Form =Majority of natural DNA ◦ Sugar-phosphate backbones of 2 strands slightly offset from helical center ◦ Forms grooves of different sizes ◦ Major Groove = capable of binding proteins with high levels of specificity ◦ Minor Groove= partially blocked by sugar moieties B-form can be transitioned into the A-form ◦ Reversible; occurs at relative humidity