Written Assignment 2

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On a rainy night in November 1998, two young women were attacked in Baltimore. One was able to escape, but the other was stabbed to death. Although it was dark and she was able to see the attacker for only a few seconds, the surviving victim was able to give police a description that enabled them to produce a sketch. A week later, a friend of the victims contacted the police, saying that he recognized the man in the sketch. He identified 24-year- old Malcolm Bryant and, in a photographic line-up the surviving victim identified Bryant as the man who attacked her. Based on the eyewitness identification, Bryant was arrested and charged with first-degree murder. Although multiple witnesses testified that Bryant was in a nightclub at the time of the crime, a jury convicted him and sentenced him to life in prison. Bryant maintained his innocence, but his appeals were all rejected. In 2011 and again in 2015, attorneys from the Innocence Project successfully petitioned to get DNA testing done on evidence that had been collected at the time of the crime. Ultimately, forensic scientists were able to obtain a full DNA profile from the T-shirt of the murder victim. This profile matched a partial profile from skin under the fingernails of the victim. It also did not match Malcolm Bryant’s DNA, providing strong evidence that he was not the murderer. His wrongful conviction was dismissed and in 2016, after more than 16 years in prison, Malcolm Bryant was released (Figure 6-1). Malcolm Bryant is one of 367 unjustly imprisoned people in the United States (as of late 2019) who have been freed from prison as a result of DNA analyses. They spent an average of 14 years behind bars. Eighty percent had been convicted of sexual assault; 36% had been convicted of murder. In 70% of the cases, inaccurate eyewitness testimony played an important role in the guilty verdict. (Recall, from Chapter 1, the experiments that revealed the unreliability of eyewitness identification.)

The importance of DNA goes far beyond its function as an individual identifier, however. The information carried within this molecule, which is organized into individual units called genes, is among the most important of all biological knowledge. And, as witnessed by these headlines, it is often in the news.

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Beginning in the 1900s and continuing through the early 1950s, a series of experiments revealed two important features of DNA. First, molecules of DNA are passed down from parent to offspring. Second, the instructions on how to create a body and control its growth, development, and behavior are encoded in the DNA molecule. Many formidable scientists rose to the challenge to determine the chemical structure of DNA and to understand how the molecule was assembled and shaped so that it could hold and transmit so much information. American Linus Pauling had already won a Nobel prize in chemistry for his work on elucidating the structure of molecules when he began investigating the structure of DNA. Simultaneously, Maurice Wilkins and Rosalind Franklin in England devoted their research to this task as well, and produced X-ray pictures of DNA that were critical to decoding its shape. But it was Francis Crick and James Watson, working in Cambridge, England, who happened to put all the pieces together and deduce the exact structure of DNA. As soon as they figured out DNA's structure, the answers to several other thorny problems in biology—such as how DNA material might be able to duplicate itself—became apparent immediately. We explore that process later in this chapter, but first we need to examine the structure of DNA in more detail.

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DNA (deoxyribonucleic acid) is a nucleic acid, a macromolecule that stores information. It consists of individual units called nucleotides which have three components: a molecule of sugar, a phosphate group (containing four oxygen atoms bound to a phosphorous atom), and a nitrogen-containing molecule called a base. The physical structure of DNA is frequently described as a “double helix.” What exactly is a double helix? Picture a long ladder twisted around like a spiral staircase and you’ll have a good idea of what a DNA molecule looks like. The molecule has two distinct strands, like the vertical sides of a ladder. These are the “backbones” of the DNA molecule, and each is made from two alternating molecules: a sugar, then a phosphate, then another sugar, then a phosphate, and so on. The sugar is always deoxyribose, and the phosphate molecule is always the same, too. It is the shapes of the molecules in the backbone that cause the DNA “ladder” to twist. The alternating sugars and phosphates hold everything in place but they play only a supporting role. The rungs of the ladder are where things get interesting. Attached to each sugar and protruding like half of a rung on the ladder, is a molecule called a base. Each sugar always has a base attached to it, and there are four different bases—adenine, thymine, cytosine, and guanine. When discussing DNA, these bases are usually referred to by their first letter: A, T, C, and G. The other side of the ladder also has bases protruding from each sugar. The base from one side of the ladder binds, via a hydrogen bond, to a base from the other side; together these base pairs form the rungs of the ladder. They don't just pair up at random, though. Every time a C protrudes from one side, it binds to a G on the other side (and vice versa: a G always binds to a C). Similarly, every time a T protrudes from one side, it binds to an A on the other side (and vice versa). For this reason, each DNA molecule always has the same number of G’s and C’s, and the same numbers of A’s and T’s. Because of these base-pairing rules, it also is true that, if we know the base sequence for one of the strands in a DNA molecule, we know the sequence in the other. For this reason, a DNA sequence is described as the sequence of bases on only one of the strands.

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One of DNA’s most amazing features is that it embodies the instructions for building the cells and structures for almost every single living organism on earth (Figure 6-5). Thus, DNA is like a universal language, the letters of which are the bases A, T, C, and G. (Note that the sugar-phosphate backbone serves only to hold the bases in sequence, like the binding of a book. It does not convey genetic information.)

(Figure 6-6) The full set of DNA present in an individual organism is called its genome. In prokaryotes, including all bacteria, the information is contained within circular pieces of DNA. In eukaryotes, including humans, this information is laid out in long linear strands of DNA. Rather than having the genome contained in one super-long DNA strand, eukaryotic DNA exists as numerous smaller, more manageable pieces, called chromosomes. Humans, for example, have three billion base pairs, divided into 23 unique pieces of DNA. Because we have two copies of each (one from our mother, one from our father), we have 46 chromosomes in each cell. Within the long sequences of bases in a cell’s DNA molecules are relatively short sequences, on average about 3,000 bases long, called genes. You may hear the word “gene” misused in the media, as if a gene were a mysterious force controlling our bodies and behavior. Here we’ll be precise: a gene is a sequence of bases (or, more precisely, base pairs) in a DNA molecule that carries the information necessary for producing a functional end-product, usually a polypeptide or an RNA molecule. The location or position of a gene on a chromosome is called a locus. Each gene is the instruction set for producing one particular molecule, usually a protein. For example, there is a gene in silk moths that codes for fibroin, the chief component of silk. And, there is a gene in humans that codes for triglyceride lipase, an enzyme that breaks down dietary fat.

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(Figure 6-7) Within a species, individuals sometimes have slightly different instruction sets for a given protein, and these instructions can result in a different version of the same characteristic. These alternative versions of a gene that code for the same feature are called alleles—and function like alternative recipes for chocolate chip cookies. Any single characteristic or feature of an organism is referred to as a trait. For example, the color of a daisy’s petals is a trait. The instructions for producing this trait are found in a gene that controls petal color. This gene may have many different alleles within a population; one allele may specify the trait of orange petals, another may specify yellow petals, and yet another may specify purple petals (see Chapter 9). Similarly, one allele for eye color in fruit flies may carry the instructions for producing red eyes, while another, slightly different allele may have instructions for brown eyes. (Ultimately, though, the trait may be influenced not just by the genes an individual carries but by the way those genes interact with the environment, too.)

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It is debatable whether humans are the most complex species on the planet, but surely we must be more complex than an onion. Comparing the amount of DNA present in various species, in terms of both numbers of chromosomes and numbers of base pairs, however, reveals a paradox: there does not seem to be any relationship between the size of an organism’s genome and the organism’s complexity (Figure 6-8).

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In almost all eukaryotic species, the amount of DNA present far exceeds the amount necessary to code for all of the proteins in the organism. The fact is, a huge proportion of the base sequences in DNA do not code for proteins, and most of these have no known purpose. When it was first observed, some biologists even referred to this noncoding DNA as “junk DNA.”

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Bacteria and viruses tend to have very little noncoding DNA; genes make up 90% or more of their DNA. It is in the eukaryotes (with the exception of yeasts) that we see an explosion in the amount of noncoding DNA (Figure 6-10). Noncoding regions of DNA often take the form of sequences that are repeated, sometimes thousands (or even hundreds of thousands) of times; often these repeats exist because some DNA sequences can make copies of themselves and the copies can move about throughout the genome. Occasionally, the noncoding DNA consists of gene fragments, duplicate versions of genes, and “pseudogenes” (sequences that evolved from actual genes but accumulated mutations that made them lose their protein-coding ability). About 25% of the noncoding regions occur within genes—in which case they are called introns. About 75% of the noncoding regions occur between genes.

In the end, the presence of this noncoding DNA is still not completely understood. Recent evidence reveals, however, that some of the “noncoding” DNA does encode extremely short RNA molecules (~20 nucleotides long) that function in gene regulation; they act as a “switch” that regulates when genes are turned on or off, or as a “volume knob” that influences the amount of the gene products produced. Noncoding DNA may also serve as a reservoir of potentially useful sequences. In any case, the label “junk DNA” is a bad description.

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