Chapter 1 The Genetic Code of Genes and Genomes

1.1 DNA is the molecule of heredity Inherited traits are determined by the elements of heredity (genes), that are transmitted from parents to offspring in reproduction Genes are composed of the chemical deoxyribonucleic acid or DNA Figure 1.6: Molecular structure of a DNA double helix

1.1 DNA is the molecule of heredity DNA was discovered by Friedrich Miescher in 1869 In 1920s microscopic studies with special stains showed that DNA is present in chromosomes In 1944 Avery, McLeod, and McCarty provided the first evidence that DNA is the genetic material

Avery, McLeod, McCarty Experiment Avery, McLeod and McCarty identified the chemical substance responsible for changing rough, non-virulent cells of Streptococcus pneumoniae (R) into smooth encapsulated infectious cells (S): Transforming activity was destroyed by DNAse, not RNAse or protease Conclusion: transforming factor that converts R cells to S cells is DNA

Figure 1.2: Griffith’s experiment demonstrating bacterial transformation

Figure 1.3: DNA is the active material in bacterial transformation.

Hershey-Chase Experiment In 1952 Hershey and Chase showed that DNA, not protein, is responsible for phage activity in bacterial cells: Radioactive phage DNA enters bacteria after attachment, but protein coat of virus remains outside Phage DNA directs the reproduction of virus in infected bacterial cells Figure 1.5: T2 phages infecting a cell of E. coli © Oliver Meckes/E.O.S./MPI Tubingen/Photo Researchers, Inc.

Figure 1.4: The Hershey–Chase experiment demonstrated that DNA is responsible for directing the reproduction of phage T2

1.2 The Structure of DNA is a double helix composed of two intertwined strands In 1953 Watson and Crick proposed the three- dimensional structure of DNA A central feature of double-stranded DNA is complementary base pairing. DNA is a double-stranded helix comprised of a linear sequence of paired subunits: nucleotides Each nucleotide contains any one of four bases: adenine, thymine, guanine, and cytosine

Figure 1.6: Molecular structure of a DNA double helix

DNA structure is a double helix DNA backbone forms right-handed helix Each DNA strand has polarity = directionality The paired strands are oriented in opposite directions = antiparallel DNA molecule showing the antiparallel orientation of the complementary strands

DNA Replication Watson-Crick model of DNA replication: The strands of the original (parental) duplex separate Each parental strand serves as a template for the production of a complementary daughter strand by means of A-T and G-C base pairing

Figure 1.7: Replication in a long DNA duplex as originally proposed by Watson and Crick

Genes and Proteins The genetic information contained in the nucleotide sequence of DNA specifies a particular type of protein Enzymes = proteins that are biological catalysts essential for metabolic activities in the cell Metabolites = small molecules upon which enzymes act In 1908 Archibald Garrod proposed that enzyme defects result in inborn errors of metabolism = hereditary diseases

Genes and Proteins Garrod studied alkaptonuria and identified the abnormal excreted substance = homogentisic acid Alkaptonuria results from a metabolic defect that blocks the conversion of a substrate molecule to a product molecule in a biochemical pathway due to the absence of a required enzyme = metabolic block In the case of alkaptonuria, a defective homogentisic acid 1,2 dioxygenase is unable to convert homogentisic acid into 4-maleylacetoacetic acid in the pathway for the breakdown of phenylalanine and thyrosine

Figure 1.8: Urine from a person with alkaptonuria turns black Courtesy Daniel De Aguiar

Genes and Proteins Another defective enzyme in the same pathway, phenylalanine hydroxylase (PAH), leads to phenylalanine accumulation which causes the condition known as phenylketonuria (PKU) Incidence of PKU, characterized by severe mental retardation, is about one in 8000 among Caucasian births. A defective enzyme results from a mutant gene

Figure 1.9: Metabolic pathway for the breakdown of phenylalanine and tyrosine

Figure 1.10: Inborn errors of metabolism in the breakdown of phenylalanine and tyrosine

Genes and Proteins In the 1940s George W. Beadle and Edward L. Tatum, using a filamentous fungus Neurospora crassa, demonstrated that each enzyme is encoded in a different gene. Their experimental approach, now called genetic analysis, led to the one gene–one enzyme hypothesis.

Figure 1.11: Beadle and Tatum obtained mutants of the fi lamentous fungus Neurospora crassa

Genes and Proteins Figure 1.12A: Mutant spores can grow in complete medium but not in minimal medium

Figure 1.12B: Each new mutant is tested

Figure 1.12C: Mutants that can grow on minimal medium supplemented with amino acid are tested

Figure 1.12D: Mutants unable to grow in the absence of arginine are tested with likely precursors of arginine

Figure 1.13: Metabolic pathway for arginine biosynthesis inferred from genetic analysis of Neurospora mutants

Complementation A mutant screen is a large-scale, systematic experiment designed to isolate multiple new mutations affecting a particular trait Mutant screens sometimes isolate different mutations in the same gene. A complementation test brings two mutant genes together in the same cell or organism.

The Principal of Complementation If this cell or organism is nonmutant, the mutations are said to complement one another and it means that mutations are in the different genes. If the cell or organism is mutant, the mutations fail to complement one another, and it means that mutations are in the same gene.

Figure 1.14: Molecular interpretation of a complementation test using heterokaryons

Figure 1.15: A method for interpreting the results of complementation tests

Complementation A gene is defined experimentally as a set of mutant alleles that make up one complementation group. Any pair of mutant alleles in such a group fail to complement one another and result in an organism with a mutant phenotype.

Central Dogma Central Dogma of molecular genetics: DNA  RNA  Protein DNA is the informational molecule that does not code for protein directly but rather acts through an RNA intermediate DNA codes for RNA = transcription RNA codes for protein = translation

Figure 1.16: DNA sequence coding for the first seven amino acids in a polypeptide chain

Figure 1.17: The “central dogma” of molecular genetics: DNA codes for RNA, and RNA codes for proteins

Figure 1.18: A DNA strand is being transcribed into an RNA strand Transcription Transcription is the production of an RNA strand that is complementary in base sequence to a DNA template = messenger RNA (mRNA) RNA contains the base uracil in place of thymine and the sugar ribose instead of deoxyribose RNA is synthesized from template DNA following strand separation of the double helix Figure 1.18: A DNA strand is being transcribed into an RNA strand

Base pairing in DNA and RNA Complementary base pairing specifies the linear sequence of bases in RNA Adenine pairs with uracil; thymine pairs with adenine; guanine pairs with cytosine

Translation The sequence of bases in mRNA codes for the sequence of amino acids in a polypeptide The mRNA is translated in a nonoverlapping group of three bases = codons that specify the sequence of amino acids in proteins Each codon specifies one amino acid Transfer RNAs (tRNA) contain triplet base sequences = anticodons, which are complementary to codons in mRNA

Figure 1.19: mRNA in translation is to carry information contained in a DNA bases to a ribosome

Translation Translation occurs at the ribosomes which contain several types of ribosomal RNA (rRNA) tRNAs participate in translation by carrying amino acids and positioning them on ribosomes Translation results in the synthesis of a polypeptide chain composed of a linear sequence of amino acids whose order is specified by the sequence of codons in mRNA

Figure 1.16: DNA sequence coding for the first seven amino acids in a polypeptide chain

Table 1.1 The Standard Genetic Code

Mutations Mutation refers to any heritable change in a gene The change may be: substitution of one base pair in DNA for a different base pair; deletion or addition of base pairs Any mutation that causes the insertion of an incorrect amino acid in a protein can impair its function

Figure 1.20: The central dogma in action

Figure 1.21: The M1V mutant in the PAH gene

Figure 1.22: The R408W mutant in the PAH gene

Genes and Environment One gene can affect more than one trait = pleiotropy Any trait can be affected by more than one gene as well as environment Most complex traits are affected by multiple genetic and environmental factors Often several genes are involved in genetic disorders and the severity of a disease may depend upon genetic status and environmental factors

Figure 1.23: Cats with white fur and blue eyes have a high risk of being born deaf, a pleiotropic effect © Medioimages/Alamy Images

Evolution All creatures on Earth share many features of the genetic apparatus and many aspects of metabolism Groups of related organisms descend from a common ancestor Evolution occurs whenever a population of organisms with a common ancestry gradually changes in genetic composition over time

Figure 1.24: Evolutionary relationships as inferred from similarities in DNA sequence Courtesy of Andrew J. Roger, Alastair B. Simpson, and Mitchell L. Sogin

Evolution The totality of DNA in a single cell = genome The complete set of proteins encoded in the genome = proteome Genes or proteins that derive from a common ancestral sequence via gene duplication = paralogs Genes that share a common ancestral gene via speciation = orthologs The molecular unity of life is seen in comparisons among genomes and proteomes

Table 1.2 Comparisons of Genomes and Proteomes