Chapter 1The Genetic Code of Genes and Genomes

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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

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• 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

1.1 DNA is the molecule of heredity

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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

5Figure 1.3: DNA is the active material in bacterial transformation.

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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.

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• 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

1.2 The Structure of DNA is a double helix composed of two intertwined strands

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• DNA backbone forms right-handed helix

• Each DNA strand has polarity = directionality

• The paired strands are oriented in opposite directions = antiparallel

DNA structure is a double helix

Figure 6.7: DNA molecule showing the antiparallel orientation of the complementary strands

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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

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

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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

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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

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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

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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.

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Genes and Proteins

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

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Figure 1.12B: Each new mutant is tested

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

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

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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.

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• 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.

The Principal of Complementation

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Figure 1.14: Molecular interpretation of a complementation test using heterokaryons

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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.

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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

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

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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

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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

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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

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

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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

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

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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

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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

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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

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Figure 1.24: Evolutionary relationships as inferred from similarities in DNA sequence

Courtesy of Andrew J. Roger, Alastair B. Simpson, and Mitchell L. Sogin

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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