Study Guide

DNA Structure, Replication, and Technology Themes

  • Evolution

    The original study of evolution by Charles Darwin, which was based on his research on various species in the Galapagos and other islands of the Pacific Ocean, was the first time that evolution was systematically studied among various species. After the work of Gregor Mendel identifying genes as the unit of inheritance, and Thomas Hunt Morgan localizing genetic information to DNA, it became clear that DNA is the driving force of evolution. Mutations in DNA, particularly genetic mutations, provide the variation necessary for natural selection. Mutations create pools of variation in DNA, and the environment and other selective pressures select for specific mutants, which is how evolution occurs.

    Most organisms with DNA genomes, such as all eukaryotes, prokaryotes, archaea, and some viruses, have a much lower mutation rate in their genomes than RNA viruses do in their genomes. Most DNA polymerases have mechanisms to fix errors in replication, while few RNA polymerases do. RNA synthesis is often a throwaway process. If you make an RNA that has too many errors, you degrade it or throw it away. DNA takes the approach of actually fixing the errors.

    A well-supported theory of evolution is that all life on Earth originated from an RNA-based ancestor, or the "RNA World" hypothesis. RNA is quite amazing because it can both function as a genetic coding molecule and as an enzyme to catalyze reactions. Because of the dual functionality of RNA, many believe that the original "life" on earth was self-replicating RNA molecules. These molecules evolved and began to gain functions, to the point that some organisms began using DNA as their genomes, and had RNAs function as enzymes or coding molecules for proteins.

    All of this is speculation, but it is an interesting theory that organisms may require better proofreading, and DNA replication requires more proofreading, which is why DNA became the dominant genetic molecule instead of RNA. Most likely, DNA polymerase developed a low-level mutation rate due to years of selection against lethal mutations. However, the rate of DNA mutation is low enough that there is some level of evolution even within the human population.

    One example of human evolution is in the prion protein, which is the causative agent for kuru, a disease of the brain. Kuru is a disease common in Pacific Islanders because it is spread by consumption of brain tissue, and cannibalism is common in that region. Due to the prevalence of kuru in this region, a mutation in the prion protein renders individuals immune to kuru. Therefore, Pacific Islanders have evolved to be even more efficient at cannibalism. Watch out next time you are in Tahiti! Just kidding, Tahitians are lovely—just make sure you have a little extra food on hand.

    However, when we think of our genome, so little of it is devoted to actual genes. Why have we evolved to have such a small portion of our genome devoted to genes? One possible theory is that having such a large genome allows us to easily add new genetic information. As complex organisms, eukaryotes more often evolve through duplication of genes and variation of duplicated genes, such as the various immunoglobin genes that make antibodies. Most gene duplication events occur as a function of a retrotransposition event or as an error in homologous recombination. Forming paralagous genes, or genes that have specialized within an organism after being duplicated, might be a more useful adaptation than a single mutation in a given gene, which might explain the abundance of retroelements in our genomes. Viruses and some bacteria, on the other hand, have small genomes, and single mutations in a gene dramatically affect their functions. Altogether, the study of evolution and DNA replication goes hand-in-hand.

  • Levels of Organization

    DNA is convenient for living things to use due to its clearly defined levels of organization. At the molecular level, there are 4 nucleotide bases: adenine, guanine, cytosine, and thymine, which are all linked to a ribose sugar and phosphate backbone. These nucleotides are joined in various sequences that are highly important for determining the genetic information that they encode. These strings of double-stranded nucleotides form what we call DNA in most organisms. If left unpackaged, the amount of DNA in a eukaryotic organism would not fit into a eukaryotic cell.

    Therefore, higher levels of organization are necessary, such as the wrapping of DNA around histone proteins, forming a nucleosome core. These nucleosomes are further wrapped around each other to condense into what we call a chromatin fiber. The chromatin fiber condenses into what we identify as a chromosome in eukaryotic cells. This level of condensation only exists during mitosis and meiosis, where it is important that there be no stray bits of DNA floating around. When you move, you make sure to put everything into boxes, and that is exactly what the cell is doing. When it divides, it wants to make sure each daughter cell has the right amount and type of DNA necessary for survival.

    However, most of the life of the cell is spent outside of mitosis (in interphase), so the levels of packaging are quite variable. Depending on the needs of the cell, certain regions of the chromosome are heavily packaged to silence them and prevent transcription from taking place, while other regions that make important proteins are loosely packaged and open for RNA transcription. This variable packaging process is important for regulating RNA transcription of various genes.

    Another level of organization in eukaryotic cells is the presence of the nucleus. The fact that all the DNA in the cell is found only in the nucleus, though some exists in the mitochondria—that is a story for another day—while all the machinery for making proteins like ribosomes are only in the cytoplasm, provides another tight level of regulation. The amazing part of eukaryotic cells is the intricate ballet that leads to protein expression. This ballet in eukaryotic cells causes them to evolve at a slower rate than prokaryotic cells and viruses; there are many checkpoints that must be cleared for protein expression to take place in the eukaryotic cell.

    Prokaryotic cells, with all due respect, are like our sloppy cousins because they lack the levels of organization that eukaryotes do. They do not have a nucleus, so their DNA, RNA, and ribosomes can all easily interact. In fact, their transcription and translation machinery occurs simultaneously, which potentially leads to damaging consequences if there are any errors in RNA transcription. Their chromosomes are also not tightly packaged because prokaryotes lack histones, and they typically have extrachromosomal plasmids that can integrate into the chromosome or can be removed. It almost seems like prokaryotes were designed to make mistakes because, unlike most eukaryotes, survival of prokaryotes is more heavily biased toward success of the species. Therefore, mutations that lead to death of specific individuals are more tolerated in prokaryotes than in eukaryotes, primarily due to the shorter life span of prokaryotes. Prokaryotes are more accepting of death, like emo vampires.