Important features of the genome and proteome
Important features of the genome and proteome:
1) Segments of nucleic acid that code for a useful sequence can be re-used, and need not arise de novo for each protein in an organism’s proteome.
2) The original genetic code probably employed 2 not 3 bases to code for each amino acid, and there were probably less than 20 constituent amino acids in primordial proteomes.
3) Many codons – the 2 or 3 base coding sequences – overlap with one another. That is, several sequences may code for a single amino acid within the polypeptide. This redundancy feature protects the proteome from random point mutations in the genome. For example, these are the triplet codons for arginine: CGU CGC CGA CGG AGA AGG
4) The function of proteins depends upon their tertiary and quaternary (3D) structure, and not on the primary (amino acid sequence) structure.
5) Homologous proteins, those that perform similar functions in different organisms, share sequences that are evolutionarily invariant, or conserved. Other amino acids may be substituted into the sequences whose sole function is to connect the important sequences without altering the 3D configuration or function of a protein.
6) Many small RNAs are important as enzymes and in epigenetic regulation – these RNAs are coded for by segments of DNA that do not code for proteins. Translation of RNA to protein is orchestrated by RNA and proteins.
7) Because the sequences of bases in RNA and one strand of DNA are complementary, the sequences of bases in RNA are equivalent to those in the other strand of DNA (with RNA's U switched to DNA's T). This means that RNA could have provided the template for encoding of its own sequences, thus eliminating any need for re-invention of a DNA code from which to transcribe RNAs.
8) The enormous number of different sequences of bases in the hypothetical 26 base RNA strand in the example demonstrates the possible ‘experiments’ that could be performed in a primordial soup mix. Remember that the example merely examined permutations and combinations for a 26 base nucleic acid polymer.
1) Segments of nucleic acid that code for a useful sequence can be re-used, and need not arise de novo for each protein in an organism’s proteome.
2) The original genetic code probably employed 2 not 3 bases to code for each amino acid, and there were probably less than 20 constituent amino acids in primordial proteomes.
3) Many codons – the 2 or 3 base coding sequences – overlap with one another. That is, several sequences may code for a single amino acid within the polypeptide. This redundancy feature protects the proteome from random point mutations in the genome. For example, these are the triplet codons for arginine: CGU CGC CGA CGG AGA AGG
4) The function of proteins depends upon their tertiary and quaternary (3D) structure, and not on the primary (amino acid sequence) structure.
5) Homologous proteins, those that perform similar functions in different organisms, share sequences that are evolutionarily invariant, or conserved. Other amino acids may be substituted into the sequences whose sole function is to connect the important sequences without altering the 3D configuration or function of a protein.
6) Many small RNAs are important as enzymes and in epigenetic regulation – these RNAs are coded for by segments of DNA that do not code for proteins. Translation of RNA to protein is orchestrated by RNA and proteins.
7) Because the sequences of bases in RNA and one strand of DNA are complementary, the sequences of bases in RNA are equivalent to those in the other strand of DNA (with RNA's U switched to DNA's T). This means that RNA could have provided the template for encoding of its own sequences, thus eliminating any need for re-invention of a DNA code from which to transcribe RNAs.
8) The enormous number of different sequences of bases in the hypothetical 26 base RNA strand in the example demonstrates the possible ‘experiments’ that could be performed in a primordial soup mix. Remember that the example merely examined permutations and combinations for a 26 base nucleic acid polymer.
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Allopatric speciation occurs when a geographical barrier sub-divides a parent species, resulting in geographic and reproductive isolation such that the descendent species can no longer interbreed upon removal of the barrier.
Anagenesis differs from cladogenesis in that one species progressively transforms into a replacement species when sufficient gene mutations fix in the descendant population. At this point, the ancestral species has become extinct. This mechanism is distinct from the increase in numbers of species generated by cladogenetic branching events.
Cladogenesis is the mechanism of speciation in which one or more lineages (clades) arise from an ancestral line. Such speciation events increase the variety of plants or animals through branching of the phylogenetic tree. Cladogenesis is differentiated from anagenesis, which is the in toto replacement of one species by an anatomically distinct species.
Monophyletic taxon or clade: an accurate grouping of only (opp. polyphyletic) and all (opp. paraphyletic) descendents of a shared common ancestor. A monopyletic group is genetically homogeneous and reflects evolutionary relationships.
Paraphyletic taxon or clade: a monophyletic group that excludes one or more discrete groups descended from the most recent common ancestral species of the entire group. Other descendent species of the most recent common ancestor have been excluded from the paraphyletic taxon, usually because of morphologic distinctiveness.
Phenetic system: groupings of organisms based on mutual similarity of phenotypic (physical and chemical) characteristics. Phenetic groupings may or may not correlate with evolutionary relationships.
Phylogenetic system: groups organisms based on shared evolutionary heritage. DNA and RNA sequencing techniques are considered to give the most meaningful phylogenies.
Phylogenetic separation into evolutionary relationships (clades), based on comparison of genomes is likely to supplant phenotypical (phenetic) taxonomies of the prokaryotes.
Peripatry (paripatry) is a subset of allopatry in which an isolated group has a smaller population than the parent group. Ernst Mayr introduced the term. Peripatric speciation occurs when the smaller sub-group of a species enters a novel niche within the range of the parent species, becoming geographically and reproductively isolated. Peripatric speciation (paripatric) is distinguished from allopatric speciation by the smaller size of the isolate group, and from sympatric speciation, which involves no barrier to breeding.
Polyphyletic taxon: opposite to monophyletic taxon: A polyphyletic group is mistakenly or improperly erected on the basis of homoplasy.—characteristics that have arisen despite not sharing a common ancestor. Homoplasy arises because of convergent evolution, parallelism, evolutionary reversals, horizontal gene transfer, or gene duplications. Polyphyletic taxa are genetically heterogeneous because members do not share a common ancestor.
Neontology is a branch of biology that emphasizes the study of modern biota (living or recent organisms) rather than fossilized organisms (paleontology).
Numerical Taxonomies are a common approach to phenetic taxonomy that employ a number of phenotypic characteristics to generate similarity coefficients that may be mapped in dendrograms. Groupings based on numerical taxonomy may or may not correlate with evolutionary relationships.
Taxonomies aim to group organisms according to shared characteristics against the background of biological diversity.
Sympatry involves no geographical separation of sub-populations of individuals. Sympatric speciation events occur most often in plants by the mechanism of polyploidy in which the number of chromosomes is doubled or tripled. John Maynard Smith proposed a model called disruptive speciation, in which homozygotes might have greater fitness than heterozygotes under some environmental conditions.