S3: “Meet the Molecules”
description
Transcript of S3: “Meet the Molecules”
S3: “Meet the S3: “Meet the Molecules”Molecules”
Nuclear genesNuclear genes ITS = ribosomal internal ITS = ribosomal internal transcribed spacertranscribed spacer
Glu = Polyphenolic adhesive protein Glu = Polyphenolic adhesive protein
Mitochondrial geneMitochondrial gene CO3 = Cytochrome c oxidase subunit CO3 = Cytochrome c oxidase subunit IIIIII
The moleculesThe molecules1.1. ITSITS = the internal transcribed spacer of the = the internal transcribed spacer of the
nuclearnuclear ribosomal genes ribosomal genes Ribosomal genes code for rRNARibosomal genes code for rRNA Spacer regions are transcribed but then removedSpacer regions are transcribed but then removed Region has restriction site polymorphism between speciesRegion has restriction site polymorphism between species
http://fp.bio.utk.edu/
mycology/Techniques/mt-what_dna.htm
DNADNARNARNA
Ribosome Ribosome (RNA + proteins)(RNA + proteins)
ITSITS
DNADNA
RNARNA
Ribosome Ribosome (RNA + proteins)(RNA + proteins)
http://fp.bio.utk.edu/mycology/Techniques/mt-what_dna.htm
http://fp.bio.utk.edu/mycology/Techniques/mt-what_dna.htm
(1809 bp total)(1809 bp total) (1341 bp total)(1341 bp total)
(303-321)(303-321)(1781-1799)(1781-1799)
ITSITS
Multiple copies in genome = many targets for PCRMultiple copies in genome = many targets for PCR
ITSITS
M. galloprovincialis (~959 bp)
| 442 | 156 | 172 | 189 | M. trossulus (~951 bp)
| 197 | 240 | 156 | 169 | 189 |
ITSITS
Restriction sites and fragment lengths for Restriction sites and fragment lengths for the the MytilusMytilus ITS locus using ITS locus using Hha IHha I restriction enzymerestriction enzyme
ITS is under less selection ITS is under less selection more variable! more variable! Reference: Braby & Somero, 2005, Marine BiologyReference: Braby & Somero, 2005, Marine Biology
PCR product
M. galloprovincialis (~959 bp)
| 442 | 156 | 172 | 189 | M. trossulus (~951 bp)
| 197 | 240 | 156 | 169 | 189 |
ITSITS
442240197
The moleculesThe molecules
2.2. Glu Glu == Polyphenolic adhesive protein - Polyphenolic adhesive protein - nuclearnuclear
Mefp-1 proteinMefp-1 protein One of the glues that attaches byssal threads One of the glues that attaches byssal threads
to rocksto rocks Number of repeats (and therefore gene length) Number of repeats (and therefore gene length)
varies between speciesvaries between species
protein
= repeat
http://biomaterials.bme.northwestern.edu/mussel.asp
GluGlu Adhesive proteins Adhesive proteins anchor byssal treads anchor byssal treads to hard surface to hard surface
At least five At least five different proteins different proteins
Many variants of each Many variants of each Most studied foot Most studied foot protein is Mefp-1protein is Mefp-1
The Mefp-1 gene codes The Mefp-1 gene codes for the polyphenolic for the polyphenolic adhesive proteinadhesive protein
GluGlu
http://biomaterials.bme.northwestern.edu/mussel.asp
Collagen-like threads with adhesive proteinsCollagen-like threads with adhesive proteins
http://biomaterials.bme.northwestern.edu/mussel.asp
GluGluDOPA groups (hydroxylated tyrosines) chelate metal ions on surfaceDOPA groups (hydroxylated tyrosines) chelate metal ions on surface
Novel uses for mussel Novel uses for mussel adhesivesadhesives
Safe, natural glue for Safe, natural glue for surgeriessurgeries
Coating for medical Coating for medical implantsimplants
Tooth coating for Tooth coating for decay preventiondecay prevention
Anti-biofouling for Anti-biofouling for boatsboats
But synthesis is But synthesis is difficultdifficult StickySticky Post-translational Post-translational modificationmodification
~110 kDa
Mefp-1 proteinMefp-1 protein
Decapeptide repeats contain multipleDecapeptide repeats contain multiple Lys = Lysine = electrostaticLys = Lysine = electrostatic Hyp = Hydroxyproline = “sticky”Hyp = Hydroxyproline = “sticky” DOPA = hydroxylated tyrosine = chelatorDOPA = hydroxylated tyrosine = chelator
Repeats vary in number with ≤ 80/proteinRepeats vary in number with ≤ 80/protein
Ala-Lys-Pro-Ser-Tyr-Hyp-Hyp-Thr- DOPA-Lys
Mefp-1 geneMefp-1 gene
Glu primers amplifyGlu primers amplify 2 products in invader 2 products in invader M. galloprovincialisM. galloprovincialis
~ 300 and 500 bp (shown above)~ 300 and 500 bp (shown above) 1 product in native 1 product in native M. trossulusM. trossulus
~ 240 bp~ 240 bp
Number of repeats (and therefore gene Number of repeats (and therefore gene length) varies between specieslength) varies between species
2502 bp2502 bp
160160
474474 654654
The moleculesThe molecules
3. CO33. CO3 = Cytochrome c oxidase = Cytochrome c oxidase subunit III - subunit III - mitochondrial mitochondrial
One subunit of a large protein in the One subunit of a large protein in the electron transport chainelectron transport chain
Species level differences are observed Species level differences are observed after DNA sequencingafter DNA sequencing
http://www.bioeng.auckland.ac.nz/images/database/bioinformatics/mitochondria.gif
MitochondriaMitochondria Organelles involved in Organelles involved in oxidative respiration oxidative respiration to produce ATPto produce ATP
Derived from bacterial Derived from bacterial endosymbionts (about endosymbionts (about 1.2 billion years ago)1.2 billion years ago)
Have genome, a Have genome, a circular DNA molecule circular DNA molecule (as in modern (as in modern bacteria)bacteria)
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html
Mitochondrial DNA Mitochondrial DNA (mtDNA)(mtDNA)
Most ancestral genes lost Most ancestral genes lost or explanted to nucleusor explanted to nucleus
Remaining genes:Remaining genes: Proteins for respiration Proteins for respiration Ribosomal genes Ribosomal genes
Mitochondrial DNA Mitochondrial DNA qualities:qualities: A haploid genomeA haploid genome Non-Mendelian inheritanceNon-Mendelian inheritance Little or no repair, Little or no repair,
therefore, evolves ~ 4 x therefore, evolves ~ 4 x faster than nuclear DNAfaster than nuclear DNA
Useful for evolutionary Useful for evolutionary studies of closely studies of closely related speciesrelated species
Complex IComplex I Complex IIComplex II Complex IIIComplex III Complex IVComplex IV
SubunitsSubunits NADH NADH DehydrogenaseDehydrogenase
Cytochrome Cytochrome bcbc11
Succinate Succinate DehydrogenaseDehydrogenase
Cytochrome c Cytochrome c OxidaseOxidase
mtDNAmtDNA 77 11 00 33nDNAnDNA 3535 1010 44 1010TOTALTOTAL 4242 1111 44 1313
http://pages.slu.edu/faculty/kennellj/
Cellular respirationCellular respiration
http://dec4.ucdavis.edu/website/Bioenergetics/
3D structure of 3D structure of cytochromescytochromes