01BIS1012012IntroLect1

01BIS1012012IntroLect1 - BIS101-001: Genes and Gene...

Info iconThis preview shows page 1. Sign up to view the full content.

View Full Document Right Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: BIS101-001: Genes and Gene Expression Welcome to BIS101-001 Winter 2012 Genes and Gene Expression R.L. Rodriguez Instructor, Mon - Wed 10:00 a.m. - 11:50 a.m. 2205 Haring Hall Introductory Lecture #1 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 1 BIS101: Genes and Gene Expression BIS101 is a survey of the fundamental concepts of genetics and molecular biology including vocabulary, technology, experiment design, with particular emphasis on gene structure and function. Prokaryotic and eukaryotic molecular models will be used to demonstrate basic principles of gene mapping, chromatin structure, genomics, replication, transcription, translation, mutations, repair, gene regulation and genetic engineering. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 2 BIS101: Genes and Gene Expression Textbook: Genetic Analysis: An Integrative Approach, Sanders and Bowman, 1st Ed. Grade based on 400 points distributed among two midterms, each worth 100 points and a final exam worth 200 points. Requests for regards should be submitted to the Teaching Assistants using a Petition for Regrade Form obtained on SmartSite. Past grade distribution is as follows: 18% As, 33% Bs, 29% Cs, 10% Ds and 8% Fs. Zero tolerance for cheating January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 3 BIS101: Genes and Gene Expression There are no early, late or makeup exams. A valid medical excuse is the only basis for missing an exam or for petitioning for an incomplete (I) grade. In the case of missed midterm exams, the final exam will be weighted an additional 100 points. Fifty (60) minutes are allotted to each midterm exam. Final exam will be cumulative: approx. 50% (100 points) from the first two midterms and 50% (100 points) based on new material. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 4 Chapter 1: Genetics enters its second century Biological information is encoded in DNA (genotype). Biological function is the result of proteins and RNAs (phenotype). Complex biological systems are the result of gene networks and interactions involving DNA-Protein, Protein-Protein, RNA-Protein). All life forms use similar mechanisms to regulate genes. The modular nature of the genome facilitates rapid evolution The analytical tools of genomics and "multi-scale" approaches, permits the dissection of the complex genetic processes for the benefit of humankind. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 5 Why Genes, Gene Expression and Genomes Course objective: To understand the true relationship between genotype and phenotype. Definition of Genotype: The actual alleles (alternation forms of a gene, or sequence of DNA) in an individual. Definition of Phenotype: An observable characteristic (produced by the genotype). Challenge: The path from genotype to phenotype is not linear! January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 6 From Genotype to Phenotype The path from genotype to phenotype is complex and nonlinear January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 7 Filters of Genetics Variation ics n et n tio tri ige Nu Ep GENOTYPE ult C re u e tyl s fe Li PHENOTYPE PHENOTYPE Life span Because of these gene modifiers, we do not have to be slaves to our genes nor do we have to be victims of genetic determinism. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 8 Modulators and Potentiators of Phenotype Genetic variation: Single nucleotide polymorphisms -- SNPs, copy number variants (CNV) variable number tandem repeats (VNTRs). Single gene action vs. pleiotropy, epistasis, epigenetics, networks and interactions Environmental factors (lifestyle) Genomic architecture: Genetic admixture, the epigenome. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 9 From Genotype to Phenotype Genetic Variation January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 10 What is the source of phenotypic differences? National Museum Single Nucleotide Polymorphism (SNP) of History January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 11 Sources of human genetic variation Single Nucleotide Polymorphism (SNP) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Alleles, SNPs and Heterozygosity Allele 1 Allele 1 G-C C-G A-T A-T T-A T-A A-T C-G G-C C-G C-G T-A A-T A-T C-G G-C C-G A-T A-T T-A T-A A-T C-G G-C C-G C-G T-A A-T A-T C-G Allele 1 Allele 2 G-C C-G A-T A-T T-A T-A A-T C-G G-C C-G C-G T-A A-T A-T C-G G-C C-G A-T A-T T-A T-A A-T T-A G-C C-G C-G T-A A-T A-T C-G Allele 1 Allele 3 Allele1 G-C C-G A-T A-T T-A T-A A-T C-G G-C C-G C-G T-A A-T A-T C-G A-T C-G A-T A-T T-A T-A A-T C-G G-C C-G C-G T-A A-T T-A C-G Allele 4 Allele 4 2 Allele3 A-T G-C C-G A-T A-T T-A T-A A-T T-A G-C C-G C-G T-A A-T A-T C-G A-T C-G A-T A-T T-A T-A A-T T-A C-G G-C C-G C-G T-A A-T A-T C-G January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 13 The Human Genome: A summary 3.4 billion base pairs distributed among 23 distinct chromosomes 610 million differences between any two individuals January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 14 enetic variation in the Phase II enzyme ene, UGT1A1, affects cancer risk UGT1A1 (TA5,8) Low Expression Increased risk of prostate cancer Heterocyclic amines Activated metabolites (mutagen) Phase II enzymes reduce activated metabolites Mutagenic DNA adducts Broiled, fried or barbecued meats Reduced risk of prostate cancer Adapted from Mucci et al, 2001 UGT1A1 (TA6) High Expression http://nutrigenomics.ucdavis.edu From Genotype to Phenotype Gene Networks January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 16 Complex biological systems emerge from regulatory networks January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 17 Complex biological systems emerge from regulatory networks Key Information Control Points January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 18 CAATT Enhancer Binding Protein Family of Transcription Factors (UGT1A1) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 19 From Genotype to Phenotype Environment x Gene Interactions (Lifestyle, Diet, Behavior, Culture, Socioeconomic Status) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 20 Environment x Gene Interactions Pima Indians in the US and in Mexico have the same genetic background. Pimas of Arizona have a T2DM rate approaching 50% for individuals over 45. Pimas of Mexico have T2D rates similar to US whites (~7%). The principle differences between these two groups are diet and physical activity. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 21 From Genotype to Phenotype Epigenetics/Epigenomics (a state of gene functionality that is not encoded in the DNA but is still heritable from one generation to the next and maintained through chemical modification of DNA) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 22 Epigenetics and Epigenomics "Epigenetic regulation thus facilitates the integration of intrinsic signals and environmental signals by using highly conserved enzymatic machinery for (chromatin modification)." January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 23 Higher Order DNA Structure and Interactions January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 24 Dissecting Environment from Genetics Identical or monozygotic (MZ) twins have the same genetic material. Dr. Robert J. Huskey, University of Virginia This make twins ideal for studying environmental affects. At the left are DNA profiles from four sets of twins. Which are MZ? January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 25 Affects of Epigenetic Drift on Phenotype January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 26 Lifestyle can affect gene expression and phenotype "Thus, distinct profiles of DNA methylation and histone acetylation patterns arise during the lifetime of MZ twins and may contribute to some of their phenotypic discordances and underlie their differential frequency/onset of common diseases. External factors such as smoking habits, physical activity or diet can have a long-term influence on these epigenetic modifications." Fraga et al, 2005. Proc Natl. Acad. Sci. 102;1064, Figure 1C January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 27 Epigenetic/Genomic Differences by Individual and Organ January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 From Genotype to Phenotype Genomic Architecture: Genetic Admixture January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 29 What about "genetic admixture"? Mexican American Health Professions Organization: Ashley L. Garcia, president; Lizette Gonzales, public relations; Carlos Cruz, treasurer; Elizabeth Salinas, vice president; Monique Rodriguez, secretary January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 30 Genetic Admixture -- Latinos African Native American European = "Mestizos" January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 31 Genetic Origins of Latino Ethnic Groups 100% 90% 80% 70% 7 24 19 African Native American European Percent Ancestral Contribution Admixture 60% 50% 40% 30% 20% 10% 0% 52 41 57 Choudhry S, et. al: 2006 Mexican American Puerto Rican 32 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Percent Racial Admixture 100% 80% 60% 40% 20% 0% Puerto Rican Volunteers 4 1 7 82 85 70 85 88 19 22 13 34 37 52 10 16 28 31 43 49 55 58 61 64 67 73 25 40 46 76 79 Individual subjects 1-90 100% 80% 60% 40% 20% 0% Mexican Volunteers European Native American African 28 34 13 19 37 49 52 67 10 16 22 25 43 46 55 58 64 70 73 76 79 61 82 4 7 31 40 1 91 88 Individual subjects 1-93 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 33 Genetic admixture distributed but in blocks Courtesy E. Burchard-Gonzalez 1 2 3 4 5 6 7 8 9 10 11 12 "Epistasis" "A meta-analysis of 43 gene-disease associations, 86% "A meta-analysis of 43 gene-disease associations, 86% showed this odd relationship (ie., higher disease risk in showed this odd relationship (ie., higher disease risk in populations with lower frequency of the diseasepopulations with lower frequency of the diseaseassociated allele." Ioannidis et al, 2004. Nat. Genetics associated allele." Ioannidis et al, 2004. Nat. Genetics 13 14 15 16 17 18 19 20 21 22 X Y 34 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Complex phenotypes are due to many factors Gene 1 Gene 2 Gene 3 ... Gene N Nutrition Genes Disease Phenotype Environment Environment in utero Culture Lifestyle 35 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Complex phenotypes are due to many Environmental factors Signals Schadt and Lum, 2006. J. Lipid Res. 47:2601-17 Complex phenotypes Epigenetic modifications: Reverse Engineer Genetic Networks January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 From Genotype to Phenotype From Genotype to Phenotype 36 Integrative Genomics: A Holistic View External Input Epigenotype Genotype Genome Regulatory networks modulated by signal transduction pathways RNAi microRNA transposons Regulatory networks modulated by chromatin remodeling (i.e. methylation, acetylation) Gene expression Gene expression Gene expression Phenotype / Health Outcomes Phenotype Phenotype Phenotype January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 37 The Single Gene/Magic Bullet Paradigm Magic Bullet (drug) Gregor Mendel 1822-1884 Paul Ehrlich 1854-1915 Gene Gene Product Disease Phenotype January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 38 The "Systems" Approach to Biological Processes All the other genes All the other genes I Idon't'tknow about, don know about, I Idon't'tcare about don care about Gene B Gene D Gene A Gene C Gene E List of ALL genes Biological Processes interactions Pathways Networks List of metabolites 1990 2009 39 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Systems Biology and Health (p. 635) Systems biology is the application of "omic" technologies (genomics, proteomics, metabolomics, informatics, combinatorial chemistry, etc.) to the studying biological processes. Unlike traditional biology which examines single genes or proteins in isolation, systems biology simultaneously studies the complex interaction of many levels of biological information - genomic DNA, mRNA, proteins, functional proteins, metabolites and informational pathways and networks - to understand the true relationship between genotype and phenotype. As biology becomes and information-rich science, the challenge will be to transform data into knowledge and knowledge into applications that will promote global health and a clean and stable environment. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 40 Systems biology integrates all the "omics" transcriptome protein proteome genotype gene informational networks Informatics metabolome gene expression profiling 41 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 What are the "omic" sciences? Genomics Functional Genomics Comparative Genomics Structural Genomics Metabolomics Proteomics Nutritional Genomics Glycomics Transcriptomics Lipomics Physiological Genomics Whateveromics January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 42 Chapter 1: The Study of Biological Information Biological information, fundamental to life, is encoded in DNA. q DNA is an ideal "information" molecule q Genomics is the high-throughput, massively parallel analysis of the structure, function and regulation of all genes in a cell or organism. q Genomics make genetics an information-rich science January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 43 Higher Order DNA Structure and Interactions January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 44 Characteristics of genetic material Characteristics of genetic material. In order to serve as genetic material, DNA must have the following four characteristics: q q q q 1. Chemical stability under a variety of environmental conditions (e.g., 0C to 100C and 0.01M salt to about 4 to 5M salt). DNA can be detected in a 10,000 year old mammoth or 400,000 years old plants. 2. DNA must be capable of self-replication (the ability to pass copies of itself from one generation to the next). 3. Must have the potential to store and transfer information. Triplet codons are used to code for the sequence of amino acids in proteins. 4. Genetic material must be mutable, that is, capable of undergoing rare chemical changes. Mutations provide the genetic variability for natural selection. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 45 From Genotype to Phenotype Proof that DNA is the genetic material -- Three experiments. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 46 The "Transforming Principle" (1928) In England, Fredrich Griffith performs his experiment showing that a substance that could change avirulent bacteria to virulent bacteria was heat stable. Avirulent pneumococci (R) became virulent when mixed with the remnants of heat-killed virulent pneumococci (S), a process called "transformation." This experiment set the stage for the Avery experiment, which used purified DNA to achieve the same result. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 47 1928: Griffith's "Transforming Principle" (p. 224) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 48 DNA is the Transforming Principle (p.225) (1944) Avery, McLeod, and McCarty perform their now famous experiment showing that DNA is the "transforming principle", capable of changing avirulent bacteria into virulent bacteria. This discovery was not accepted by the scientific community, however. Many still favored protein as the hereditary material, suggesting that Avery's DNA sample was contaminated with trace amounts of protein and other materials. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 49 Avery, MacLeod & McCarty Experiment (p. 225) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 50 Hershey Chase Experiment (p.226-7) (1951) Alfred Hershey joined the APG and used 32P labeled phage DNA and 35S labelled phage coat proteins to show that only 32P was transferred from parental phage to progeny phage. This experiment finally laid to rest the protein/DNA debate and demonstrated the importance of the Avery et al. discovery. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 51 1952 -- A. Hershey and E. Chase Experiment (p.226-7) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 52 Milestones of Modern Genetics (p.7) April 25, 2003 -- 50th anniversary of the discovery of DNA January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 53 Structure of DNA ...phosphate diester groups joining -Ddeoxyribofuranose residues with 3',5' linkages. linkages .... the two chains run in opposite directions. directions ...The bases are on the inside of the helix and the phosphates on the outside... ...a single base from one chain being hydrogen - bonded to a single base from the other chain ...one of the pair must be a purine and the other a pyrimidine for bonding to occur. It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. 54 January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 Models of DNA (p.231) 20 Major Groove 3.4 Stick Model Space Filling Model Minor Groove End View Rose Window St. John The Divine NYC January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 55 Chapter 1: The Study Biological Information Biological information, fundamental to life, is encoded in DNA. Biological function emerges primarily from proteins and RNAs. Complex biological systems emerge from interaction networks (DNA-Protein, Protein-Protein). All life forms are closely related (motifs) The modular nature of the genome facilitates rapid evolution Powerful analytical tools and a "systems approach" to research, permits the dissection of the complex genetic processes for the benefit of humankind. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 56 Biological function comes from proteins and RNAs January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 57 Biological function comes from proteins and RNAs January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 58 Genetic Code Links DNA to Proteins (p. 13, 314-20) January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 59 Biological function comes from proteins and RNAs Primary Structure Tertiary Structure Secondary Structure January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 60 Biological function comes from proteins and RNAs Hemoglobin quaternary structure There are may different types of proteins: Structural proteins Enzymes Regulatory proteins Receptor proteins Signaling proteins Regulatory proteins Carrier proteins Immunoglobulins January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 61 Chapter 1: The Study Biological Information Biological information, fundamental to life, is encoded in DNA. Biological function emerges primarily from proteins and RNAs. Complex biological systems emerge from interaction networks (DNA-Protein, Protein-Protein). All life forms are closely related (motifs) The modular nature of the genome facilitates rapid evolution Powerful analytical tools and a "systems approach" to research, permits the dissection of the complex genetic processes for the benefit of humankind. January 9, 2012 BIS10101 Winter 2012--Genes and Gene Expression, R.L. Rodriguez 2012 62 ...
View Full Document

Ask a homework question - tutors are online