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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 l.jpg

Plant Speciation & Evolution (PBIO 475/575)

Molecular Components

of Heredity


Dna double helix l.jpg
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)


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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


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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)


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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


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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)


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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)


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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


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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)


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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)


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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


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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!


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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)


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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


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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


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Regulatory Genes

  • "Multiple" systems—may represent multiple genes, promoters, regulators or combos of these

  • Originate from duplications, can diverge later

Langridge (1991)


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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)


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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


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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)


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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


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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


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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


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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


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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


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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


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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)


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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


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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)


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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)


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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 l.jpg
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 l.jpg
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 l.jpg
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!


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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)


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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


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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)


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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!


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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


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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.


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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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