Post on 19-Jan-2020
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Supplemental reading and links: continuously updated
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Roots of molecular ecology and tidbits from the modern synthesis
Classical view versus shifting balance
Rise of neutralism
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Definitions
Biotype: group of genetically-identical individuals, or an infraspecific group of microbes that can't be differentiated by biochemical characters
Genome: total genetic information carried by a cell or organism; In eukaryotes, the nuclear, mitochondrial, and chloroplast genomes may be considered separately
Plan for today
Basics of DNA structure and function, as related to molecular ecology
Figures from Lodish et al. 2004 and Beebee and Rowe 2004 (see supplemental reading list on website)
Significance of DNA as an Ecological Marker
Nucleic acids are shared component of all recognized life forms: same basic chemical structure
Common currency or lengua franca of life
Raw material for evolution
Genomes have signatures of integrated history of organisms from generational to evolutionary timescales
Important Features of H-BondsHydrogen bonding is readily reversible: DNA can 'melt' into single-stranded molecules and 'reanneal' into double-stranded molecules
G-C pairs have 3 bonds, A-T only 2 bonds, so G-C content of DNA is major determinant of 'melting temperature'
Non-specificity: mispairing can and does occur!
DNA and RNA Secondary StructureLinear versus circular
supercoiled versus relaxed
Single-stranded vsdouble-stranded
16S Ribosomal RNA
DNA ReplicationSemi-conservative
RNA primers from primase
DNA polymerase extends
Strands grow 5' to 3'
DNA Transcription (Gene Expression)Conversion to mRNA by RNA Polymerase
mRNA subsequently processed into transcript
mRNA ProcessingTranscribed mRNA has introns, non-translated
Modification of 5' and 3' ends (poly-A tail)
Splicing at conserved splice sites
Alternative splicing common: one gene->many polypeptides
5' and 3' Untranslatedregions (UTRs) usually variable
Translation to Proteins (cytoplasm)
Three types of RNA involved:
mRNAtransfer RNAribosomal RNA
Multiple tRNAs may exist for each codon, and one AA may bind to different tRNAs
Codons are the 'words' of the genetic code
Nuclear Genome SizeSize of nuclear genomes varies tremendously among organisms: C-value paradox
No association with organismal complexity, number of chromosomes, or number of genes Arabidopsis thaliana 120 Mbp
Poplar 460 MbpRice 450 MbpMaize 2,500 MbpBarley 5,000 MbpHexaploid wheat 16,000 MbpFritillaria (lilly family) >87,000 Mbp
Types of Repetitive DNA in Nuclear Genome
Satellites: 14 to 500 bp units covering 20-100 kb: centromeres and telomeres
Minisatellites: 20-50 repeat units, 1 to 5 kb regions
Microsatellites: 1 to 10 bp units, 5 to 100 repeats
ribosomal RNA (rRNA): (5-10 kb units, hundreds to thousands of repeats)
Transposable elements: RNA and DNA-based; highly variable among species and sometimes highly abundant
Genome Duplication
Genome duplication evolutionarily important in many (most)? organisms
Duplication often followed by extensive rearrangments: diploidization
Polyploids also persist as new species:
allopolyploids: derived from hybridsautopolyploids: doubling of chromosomes of an individual
Ribosomal RNA (DNA)Highly conserved RNA sequences associated with Ribosomal proteins, important in protein synthesis
Occur in tandem repeats in eukaryotic genomes: sometimes quite large
Number of repeats correlated with rates of protein synthesis
Important for systematics