Structural View of Biology
The major molecules of protein synthesis, from DNA to RNA to ribosomes to folded proteins, are available in the PDB archive. Proteins are built in several steps in all living organisms. The blueprint for each protein is stored in the genome, encoded in strands of DNA. This information is transcribed into an RNA copy, which is then used to construct the protein chain. After the chain is synthesized, it may be modified with special chemical groups, chaperoned into its proper folded shape, and ultimately destroyed when it is not needed any longer.
A complete copy of the DNA genome is constructed every time a cell divides. The enzyme DNA polymerase separates the two strands in the DNA double helix and builds a complementary copy to each one.
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Our genetic information is safely locked up inside the double helix of DNA. In order to use this information, the helix must be unwound to expose the bases, allowing polymerases access to build complementary DNA or RNA strands. Unwinding of DNA is trickier than you might expect. The interaction between bases is quite strong and there are many, many of them, so it takes appreciable energy to separate the strands. This is the job of DNA helicases: they are enzymes that pull apart the two strands in a DNA double helix.
Discussed StructuresDNA HelicaseDNA Helicase and a Helicase LoaderDnaA
DNA polymerase plays the central role in the processes of life. It carries the weighty responsibility of duplicating our genetic information. Each time a cell divides, DNA polymerase duplicates all of its DNA, and the cell passes one copy to each daughter cell. In this way, genetic information is passed from generation to generation. Our inheritance of DNA creates a living link from each of our own cells back through trillions of generations to the first primordial cells on Earth. The information contained in our DNA, modified and improved over millennia, is our most precious possession, given to us by our parents at birth and passed to our children.
Discussed StructuresDNA polymerase I Klenow fragmentTaq polymerasehuman DNA polymerase beta
In our genome, it takes thousands of DNA nucleotides to encode the information for each protein, and even more to store all the regulatory information. So, when a cell needs to copy this information, it has to manage long, long stretches of DNA. As you might imagine, this is not easy in the chaotic environment of the cell.
Discussed StructuresComplex of sliding clamp, clamp loader, and DNASliding clamp with FEN1 endonuclease
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