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.

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Evidence Found for Origin of Genes

Evidence Found for Origin of Genes: "Evidence compiled by a team, led by Nobel laureate Walter Gilbert, supports the theory that all genes in all organisms that ever lived on Earth consist of a small number of basic building blocks. These blocks were shuffled and recombined during the past 3-4 billion years to form a dazzling variety of simple and complex proteins that make up life as we know it. The genes carry instructions for making proteins that do everything from allowing bacteria to metabolize methane gas to aiding humans to think."

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mtDNA

The Woodstock of Evolution -- The World Summit on Evolution (ScientificAmerican.com): University of Cambridge professor Peter Forster, is an expert in archaeogenetics and states that prehistoric human migrations can be traced by mitochondrial DNA (mtDNA) through the maternal line of modern humans. These mtDNA samples are obtained by taking cheek swabs.

Mitochondrial DNA is passed down the maternal line because the oocyte contains mitochondria within the cytoplasm. Because spermatozoa contain almost no cytoplasm, and hence no mtDNA containing mitochondria, the Y chromosome is employed to trace lineages of human males.

See also, Fossil Hominids: mitochondrial DNA The Great DNA Hunt NOVA Online Neanderthals on Trial Tracing Ancestry with MtDNA Genetics and Genealogy: Y Polymorphism and mtDNA Analyses Genetics and Human Migration Patterns

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Ancient DNA

McMaster Ancient DNA Center: "Once an organism dies, presumably the single most important factor in the long-term preservation of its DNA is the rate at which specific cellular enzymes, called nucleases, can be stopped. These endonucleases are efficient and can rapidly cleave DNA into small fragments. However as these are energy requiring functions, and a cell without oxygen will deplete its energy sources quickly, nuclease degradation may cease relatively soon post mortem. The organism must then face the bacterial, fungal and insect onslaught which can be quite effective but often incomplete. Once bacterial onslaught has slowed, the DNA molecule is still subject to chemical degradation via hydrolysis and oxidation. To understand the processes which degrade the DNA molecule in the fossil record and under what conditions these reactions are minimized, one needs to look briefly at the molecule itself and its susceptible sites."

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DNA evolutionary connections

UCSD Study Shows 'Junk' DNA Has Evolutionary Importance: "In the October 20 issue of Nature, Peter Andolfatto, an assistant professor of biology at UCSD, shows that non-coding regions play an important role in maintaining an organism's genetic integrity. In his study of the genes from the fruit fly Drosophila melanogaster, he discovered that these regions are strongly affected by natural selection, the evolutionary process that preferentially leads to the survival of organisms and genes best adapted to the environment."

Intron functions: "Although some introns, such as those in globin genes, appear to be inserted at what are structural domain boundaries in the polypeptide, many intron insertion positions bear no relation to structural or functional domains. The theory that introns serve an evolutionary function in allowing the shuffling of exons is still being debated."

Group II introns: "Some group II introns have a second remarkable property: they encode reverse transcriptase (RT) ORFs and are active mobile elements. Such mobile group II introns can insert into defined sites at high efficiencies (called retrohoming), or can invade unrelated sites at low frequencies (retrotransposition).Group II introns were discovered and first studied in organellar genomes, where they are relatively abundant. However, group II introns are now being found in unexpected numbers in bacterial genomes"

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evolution and organogenesis

MOLECULAR BIOLOGY: ON HEDGEHOG PROTEINS: "It is now widely accepted that similar sets of factors are shared by different animal species and also by distinct processes in the course of early patterning of organogenesis. During animal evolution, a 'prepattern' of fundamental organs apparently emerged relatively early."

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