The DNA Story

Germs, Genes, and Genomics

4

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 ResearchGriffith & Avery

Fig. 4.2 Transformation experiments of Griffith, A-B

The Roots of DNA ResearchGriffith & 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 Roots of DNA Research

• 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

• X-ray crystallography

• Double helixFigure 4.4a: James D. Watson and Francis H. C. Crick in 1952

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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 X174.

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

Figure 4.12: President Clinton with J. Craig Venter and Francis Collins announcing the draft copy of the human genome

© AP Photos

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)