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Plant Speciation & Evolution (PBIO 475/575). Molecular Components of Heredity. DNA Double Helix. Sugar-phosphate backbone Base-pair "rungs" of ladder Nucleotides attached to S-P molecules Strands antiparallel (run in opposite directions, 5\'-->3\'). Raven et al. (1992). DNA Double Helix.

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plant speciation evolution pbio 475 575

Plant Speciation & Evolution (PBIO 475/575)

Molecular Components

of Heredity

dna double helix
DNA Double Helix
  • Sugar-phosphate backbone
  • Base-pair "rungs" of ladder
  • Nucleotides attached to S-P molecules
  • Strands antiparallel (run in opposite directions, 5\'-->3\')

Raven et al. (1992)

dna double helix3
DNA Double Helix
  • Each base-pair "rung" has a purine (A or G) and pyrimidine (C or T)
  • Strands held together by hydrogen bonds between nucleotides
  • Chemical structures of nucleotides discourage "incorrect" pairing
  • G-C pair has 3 hydrogen bonds, A-T only 2-->former is stronger
dna replication
DNA Replication
  • Semiconservative--replication results in two strands, one original and one new
  • Sequence of events
    • Helix unwinds
    • Both strands replicate simultaneously, during unwinding process

Raven et al. (1992)

dna replication5
DNA Replication
  • Sequence of events (cont.)
    • "Leading" strand replicates continuously from 3\' end
    • newest end of forming strand oriented toward replication fork
    • "Lagging" strand replicates by a series of fragments placed end-to-end, facing away from fork; fragments with newest ends of fragments later "ligated"
    • 2 polymerases "proofread" for mismatched bases
physical structure of genes
Physical Structure of Genes
  • Segments of chromatin that yield proteins through transcription, translation
  • Typically separated by stretches of inactive chromatin (intergenic spacers)
  • Commonly encompasses short stretches of inactive chromatin that get cut out during translation (introns)
  • Can experience recombination in whole or in part! (contrary to original theories)
physical structure of genes7
Physical Structure of Genes
  • Fundamental components
    • Promoter region "upstream" of initiation site
      • Necessary binding site for RNA polymerase to accomplish translation
      • Bears recognition sequences for enzyme (e.g., TTTA)
    • Initiation site for transcription--yields ribosomal binding site in mRNA

Suzuki et al. (1989)

gene structure and function
Gene Structure and Function
  • Fundamental components (cont.)
    • Coding region (exon) of structural gene
      • Composed of codons (triplets) of nucleotides
      • Begins with start codon (e.g., TAA)
      • Ends with stop codon
      • Codons complementary to mRNA codons

--> amino acids in ultimate protein chain

    • Termination region--halts polymerase from transcribing
transcription
Transcription
  • Transcription from DNA strand in nucleus
    • Takes place in three areas of DNA strand
      • One site codes for large & small subunits of rRNA
      • Second site downstream codes for tRNAs
      • Third site further downstream codes for proteins
    • Nucleotides assembled parallel to DNA
    • Complementary nucleotides used: A<-->U, C<-->G

Suzuki et al. (1989)

post transcriptional processes
Post-transcriptional Processes
  • Processing of primary RNA transcript from protein-coding DNA
    • 5\' cap and 3\' poly-A tail stuck on
    • introns spliced out in several stages, bringing exons into proximity
    • Processing in different organs eliminates different portions of transcript

--> different mRNA products from initial transcript

Suzuki et al. (1989)

post transcriptional processes11
Post-transcriptional Processes
  • rRNA and tRNAs move into cytoplasm through nuclear pores immediately
  • Mature mRNA moves into cytoplasm after processing completed
  • Genes of mature mRNA translated to proteins
    • Ribosomal subunits attach to mRNA (usually several at different points)
    • tRNAs bring amino acids corresponding to mRNA codons into proximity of ribosomal complex
    • Amino acids joined by peptide bonds to form protein chain
  • No "proofreading" functions by RNA polymerases
post transcriptional processes12
Post-transcriptional Processes
  • MicroRNAs (miRNAs)—newly discovered, very small RNAs that bind to trancripts and render them non-functional (Griffiths et al. [2008])
  • play potentially huge role in accomplishing heterochronic (time-shifting) or tissue-specific gene expression
  • Hundreds of loci found in typical genomes, appear to be produced from “junk” DNA regions
  • miRNA abundance and diversity influenced by environmental conditions
  • Heritable in the next generation—hence “Lamarckian” in behavior!
the genetic code
The Genetic Code
  • Degeneracy of the code
    • 4 nucleotides, organized into triplets, yield 64 possible combinations
    • 20 commonly employed amino acids
    • Multiple "synonymous" codons for many amino acids

Raven et al. (1992)

the genetic code14
The Genetic Code
  • Codon-anticodon pairing
    • Third position "wobble"--sloppy pairing for last nucleotide in codon
    • mRNA codons with G or U in third position will recognize and accept more than one tRNA anticodon
regulatory genes
Regulatory Genes
  • Determine or influence timing, placement or extent of structural gene (enzyme-producing gene) action
  • Regulation most common at the transcriptional level
    • Effects most far-reaching (especially morphologically) of all possible regulatory types
    • Results from "switching" on and off of gene transcription for particular genes
  • Simple system—encompasses some but not all genetic systems
regulatory genes16
Regulatory Genes
  • "Multiple" systems—may represent multiple genes, promoters, regulators or combos of these
  • Originate from duplications, can diverge later

Langridge (1991)

enzyme architecture
Enzyme Architecture
  • Primary--linear sequence of amino acids
  • Secondary--side-group interactions
    • alpha-helix
    • beta-pleated sheet

Computer-simulated folding of rubisco

Kellogg & Juliano (1997)

enzyme architecture18
Enzyme Architecture
  • Tertiary--folding of secondary components
  • Quaternary--multimeric associations among tertiary elements
  • Protein structure at any or all levels can impact or determine enzymatic function
enzymatic pathways
Enzymatic Pathways
  • One gene-one enzyme hypothesis
    • One gene controls production of a single enzyme
    • A biochemical reaction is catalyzed by one enzyme
    • Processes occur as a series of catalyzed reactions each ultimately regulated by a different gene

Suzuki et al. (1989)

enzymatic pathways20
Enzymatic Pathways
  • Metabolic cycles
    • e.g., photosynthesis
    • e.g., flavonoids
    • Usually slow to evolve
    • Would have been important early on in evolution of land plants
    • Increased complexity, integration-->now largely regulatory adjustments, at least among closely related species
enzymatic pathways21
Enzymatic Pathways
  • Development/morphology
    • e.g., pollination mechanisms in orchids
    • May evolve very rapidly
    • Slight changes by many different genes yield major cumulative changes-->new adaptive complexes in a radiating lineage
    • Slight individual (developmental) modifications to morphology accompanied by biochemical adjustments
regulatory vs structural genetic change
Regulatory vs. Structural Genetic Change
  • Example 1--Studies of duplicate gene expression in catastomid fishes
    • Family originated from polyploidy ca. 50 million years ago
    • 15 species now extant
    • Half of duplicated genes in polyploids have lost expression
regulatory vs structural genetic change23
Regulatory vs. Structural Genetic Change
  • Example 1--Studies of duplicate gene expression in catastomid fishes (cont.)
    • Remainder have altered in expression in 60% of tissues studied
    • Most changes in duplicate gene expression relate to different organ and tissue locations, not to cell type or developmental stage
    • Only 12/84 divergent tissue expressions traceable to enzyme-coding gene mutations
    • Most tissue-characteristic enzyme patterns have therefore resulted from mutations in transcriptional or processing stages of RNAregulatory elements
regulatory vs structural genetic change24
Regulatory vs. Structural Genetic Change
  • Example 2--Surveys of tryptophan biosynthetic pathways in protists and fungi
    • Regulation mechanisms are at least as easily modified as gene locations (=chromosome structural changes)
    • Much more readily altered than primary structure of active enzymesmore evidence of rapid changes in regulatory mechanism
regulatory vs structural genetic change25
Regulatory vs. Structural Genetic Change
  • Example 3--Hybrids between morphologically very similar taxa of fish
    • Express ontogenetic disturbances, e.g., increases in morphological abnormalities, lethality
    • Species very closely related, probably only recently diverged (not sufficient time for extensive genetic differentiation of structural genes
    • Species divergence must be in the molecular regulation of genes underlying morphological traits
organization of genetic material
Organization of Genetic Material
  • Hierarchical arrangement
    • DNA strands paired in a double helix
    • Chromatin "beads on a string"--double helix wound helically around 8-part histone molecule, as chain of "nucleosomes"
    • Nucleosomes packed into a tight "solenoid" ("supercoiling")
    • Packed stretches of nucleosomes for part of condensed chromosomes

Raven et al. (1992)

organization of genetic material27
Organization of Genetic Material
  • Multiple-copy DNA
    • Dispersed repetitive DNA
      • Scattered throughout genome
      • Minisatellites--complicated motifs, dozens/hundreds of bp long
      • Microsatellites--simple repeat motifs, usually <30 bp long
      • Considered "junk" DNA—but may accidentally become involved in transcription through accidents of replication
    • Gene families
      • Copies in different locations, i.e., on different chromosomes
      • e.g., ribosomal genes, histone genes
      • “concerted evolution” in some families homogenizes sequence across all loci—but is random in direction, can proceed with different “templates” across populations
mendelian principles
Mendelian Principles
  • Alleles--different phenotypic expressions of the same genetic trait
  • Dominance relationships
    • Complete dominance
      • Dominant allele--expresses phenotype if only one copy is present
      • Recessive allele--only expresses phenotype if both copies are present

Raven et al. (1992)

mendelian principles29
Mendelian Principles
  • Other dominance relationships
    • Incomplete dominance--intermediate phenotype in heterozygote
    • Codominance--both phenotypes expressed in heterozygote (e.g., blood types LmLm, LnLn and LmLn)
mendelian principles30
Mendelian Principles
  • Allelic systems
    • Classical 2-allele—”traditional” model
    • Multiple allelic series
      • Documented for many genes, often with non-simple relationships
      • e.g., chevron leaf pattern of white clover
      • e.g., incompatibility systems enforcing outcrossing
mendelian principles31
Mendelian Principles
  • Genotypes
    • Homozygote--both alleles are the same
      • Homozygous dominant (AA)—expresses phenotype coded by the “dominant” allele
      • Homozygous recessive (aa)—expresses phenotype coded by the “recessive” allele
    • Heterozygote--alleles are different (Aa); expresses phenotype of dominant allele if dominance relationship is “dominant” type, but something intermediate or divergent where relationship is “incomplete” or “codominant”
mendelian principles32
Mendelian Principles
  • Mendel\'s laws
    • Law of Segregation
      • Members of a gene pair segregate into separate gametes
      • One-half of the gametes has one member, the other half, the other
    • Law of Independent assortment--during gamete formation, segregation in each gene pair is independent of other pairs

Suzuki et al. (1989); Raven et al. (1992)

other genetic effects
Other Genetic Effects
  • Lethal genes
    • Death in recessive homozygote harboring lethal alleles
    • Sometimes skews progeny ratios where heterozygotes are "subvital"
  • Pleiotropy--one allele affects two or more characters, e.g., coat color and survival in yellow mice
  • Epistasis--phenotypic expression of one gene dependent on expression of another gene
  • Suppressor genes
  • Modifier genes
  • Duplicate genes
  • NOTE—many of these are “non-Mendelian” or even “non-Darwinian” in inheritance!
mitotic and meiotic products
Mitotic and Meiotic Products
  • Mitosis
    • Occurs in somatic cells
    • Yields two daughter cells from one
    • Daughters diploid, same as parent
    • Daughters typically genotypically identical to each other and to parent
  • Usually disregarded in terms of heritable variation (but consider somatic mutations affecting flower primordia)

Mitosis

Meiosis

Raven et al. (1992)

mitotic and meiotic products35
Mitotic and Meiotic Products
  • Meiosis
    • Occurs in generative cells ("sex cells")
    • Yields, ultimately, four daughter cells from one
    • Daughters haploid, reduced from diploid parent (meiocyte)
    • Daughters typically genotypically different from each other and from parent
  • Primary point where mutations are incorporated as heritable variation
crossing over
Crossing-over
  • Commonly accompanies meiosis, at the "four-strand" stage
  • Occurs usually between any two nonsister chromatids
  • Begins with intertwining of homologous chromosomes ("chiasmata")

Suzuki et al. (1989)

crossing over37
Crossing-over
  • Intertwined strands break at chiasmata and reunite, with exchange of chromosome parts
  • Typically crossing-over is equal-->same-sized fragments broken at same point and swapped, yielding structurally identical chromatids
  • 50% or fewer progeny are recombinant
  • Generates huge numbers of new recombinant genotypes, at each sexual reproductive cycle, in each individual, in each population, across the species!
crossing over38
Crossing-over
  • Multiple crossing-over events
    • Double crossing-over between adjacent sister chromatids yields double recombinants
    • Crossing-over also takes place among non-adjacent chromatids
  • Interference
    • In some areas of chromosomes double crossing-over never occurs
    • Suggests non-independence of crossing-over in some regions
bibliography
Bibliography
  • Griffiths, A. J. F., S. R. Wessler, R. C. Lewontin, and S. B. Carroll. 2008. Introduction to genetic analysis, 9th ed. W. H. Freeman and Company, New York, New York. 838 pp.
  • Kellogg, E. A. and N. D. Juliano. 1997. The structure and function of RuBisCO and their implications for systematic studies. American Journal of Botany 84:413-428.
  • Langridge, J. 1991. Molecular genetics and comparative evolution. John Wiley & Sons, Inc., New York, New York. 216 pp.
bibliography40
Bibliography
  • Raven, P. H., R. F. Evert, and S. E. Eichhorn. 1992. Biology of plants, 5th ed. Worth Publishers, New York, New York. 791 pp.
  • Suzuki, D. T., A. J. F. Griffiths, J. H. Miller, and R. C. Lewontin. 1989. An introduction to genetic analysis, 4th ed. W. H. Freeman and Company, New York, New York. 768 pp.
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