Lecture 3: Molecular Basics for Molecular Ecology

August 25, 2006

Nuts and BoltsEmail?

All components of website upLiterature: username: bio password: difazio

Supplemental reading and links: continuously updated

Office Hours: M,W,Th 1-2 pm or by appointment

Last Time

Roots of molecular ecology and tidbits from the modern synthesis

Classical view versus shifting balance

Rise of neutralism

Questions?

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

Types of Mutations (Polymorphisms)

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

Noncoding DNA is Answer

Fugu: 365 MbpHuman: 3500 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

Next Time

The organization and characterization of genetic variation in populations

Take a look at the reading for Wednesday!