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4 The DNA Story Germs, Genes, and Genomics Heredity • Genes • DNA • Manipulating DNA The Roots of DNA Research • Gregor Mendel – – – – – 1860s Pea plants Heritable traits Occur in pairs Concept of chromosomes Figure 4.1a: Gregor Mendel © National Library of Medicine The Roots of DNA Research • Thomas Hunt Morgan – 1910 – Fruit flies – Chromosomes • Willard Johannsen – Genes Figure 4.1b: Thomas Hunt Morgan © National Library of Medicine The Roots of DNA Research • Focus on DNA – 1869 Johann Fredrich Meischer • White blood cells from salmon – 1920s Alfred Mirsky • Same DNA amount in all cells – 1928 Frederick Griffith • Pneumococci • Transforming factor – 1944 Oswald Avery • DNA is transforming factor The Roots of DNA Research Griffith & Avery Fig. 4.2 Transformation experiments of Griffith, A-B The Roots of DNA Research Griffith & Avery Fig. 4.2 Transformation experiments of Griffith, C-D The Roots of DNA Research • Focus on DNA – Alfred Hershey & Barbara Chase • Radiolabeled bacteriophages • Determined that DNA is heritable material The Roots of DNA Research: Hershey & Chase Fig 4.3 Determining the function of DNA • The structure of DNA – 1920s Pheobus Levine • DNA and RNA • Existence of ribose and deoxyribose • Existence of A, T, G, C, and U – Erwin Chargaff • Amount of T equals amount of A; G equals C – 1953 Rosalind Franklin, Maurice Wilkins, James Watson, Francis Crick © Cold Springs Harbor Laboratory Archives/Photo Researchers, Inc. The Roots of DNA Research • X-ray crystallography • Double helix Figure 4.4a: James D. Watson and Francis H. C. Crick in 1952 DNA to Protein • 20 different amino acids • Over 10,000 different proteins per microbe • How does this diversity occur? DNA to Protein • The intermediary and the genetic code – – – – – – DNA in nucleus, proteins made in cytoplasm RNA present in large quantities RNA moves from nucleus to cytoplasm Information transfer DNA->RNA->protein 1961 Francis Crick: codons Determination of genetic codes for each amino acid Table 4-2: The Genetic Codes for Several Amino Acids DNA to Protein • Transcription – – – – Promoter mRNA Codons Eukaryotic mRNA • Splicing: introns and exons • 7-methyl guanosine cap • Poly-A tail DNA to Protein: Transcription Figure 4.7: The transcription process DNA to Protein • Translation – On ribosomes – Amino acids come together to form proteins, based on the code in the mRNA – tRNAs facitilate by “carrying” amino acids to the ribosome – Codon-anticodon interactions – Formation of peptide bonds between amino acids – Process repeats until termination – Further protein modifications after translation DNA to Protein: Translation Figure 4.9: A summary view of protein synthesis DNA to Protein • Gene regulation – lac operon (codes for proteins that breakdown lactose) • Absence of lactose – Repressor bound to operator – No transcription – No gene expression – No energy waste, making proteins required to break down lactose • Presence of lactose – Lactose bound to repressor – Repressor no longer bound to operator – Transcription – Gene expression – Only now making proteins required to break down lactose DNA to Protein: Gene Regulation Figure 4.10: The operon theory of gene regulation Genes and Genomics • Genomics – The study of genomes – 1977 Frederick Sanger • DNA sequencing • Exact nucleotide makeup of FX174. Genes and Genomics – Effort to map the human genome – Compare E. coli (4.7 million bases) to humans (3 billion bases) – Expansion of effort • • • • • • Escherichia coli (bacterium) Saccharomyces cerevisiae (yeast) Caenorhabditis elegans (nematode) Drosophila melanogaster (fruitfly) Zea mays (corn) Mus musculus (mouse) Genes and Genomics • The methods of genome research – Traditional method • • • • Ordering genes on chromosomes Gene linkage map Physical map Base-by-base sequencing – “Shotgun” sequencing • Fragment entire genome • Sequence each base • Reassemble entire genome from sequenced fragments Genes and Genomics: Methods of genome research Figure 4.11: Sequencing methods for determining the base sequence of a molecule of DNA Traditional method Genes and Genomics: Methods of genome research Figure 4.11: Sequencing methods for determining the base sequence of a molecule of DNA Shotgun method Genes and Genomics • Microbial genomics – 1995 J. Craig Venter and Hamilton Smith • • • • – – – – Haemophilus influenzae sequence First free-living organism to be sequenced 1.8 million bases 1749 predicted genes Mycoplasma genitalium Methanococcus jannaschii (archaea, not bacteria) Staphylococcus aureus Saccharomyces cerevisiae • Multiple chromosomes • 12 million bases • 6000 predicted genes Genes and Genomics • Microbial genomes – 1997 • • • • • Helicobacter pylori (gastric ulcers) Borrelia burgdorferi (Lyme disease) Streptococcus pneumoniae (bacterial pneumonia) Bacillus subtilis (industrial microbe) Escherichia coli (microbiological model bacterium) – 1998 • • • • Treponema pallidum (syphilis) Mycobacterium tuberculosis (tuberculosis) Caenorhabditis elegans (biological model nematode) Arabidopsis thaliana (biological model mustard plant) Genes and Genomics • The human genome – 1989: the beginning – British and American labs – 2000: Draft copy of human genome © AP Photos Figure 4.12: President Clinton with J. Craig Venter and Francis Collins announcing the draft copy of the human genome Genes and Genomics • The human genome – – – – – – – – – Human genes number 35-50,000 (lower than 100,000 prediction) About 3,164,700,000 bases, close to 3 billion estimate Average gene about 3000 bases 99.9% of DNA bases are the same in most people 50% of newly discovered genes have no known function Less than 2% of bases code for proteins Over 50% of DNA was considered “junk” Chromosome 1: 2968 genes (most) Chromosome Y: 231 genes (least)