Structure, Replication, and Transcription of DNA for AP Biology

Practice problems for these concepts can be found at: Molecular Genetics Review Questions for AP Biology

DNA Structure and Function

Deoxyribonucleic acid, known to her peers as DNA, is composed of four nitrogenous bases: adenine, guanine, cytosine, and thymine. Adenine and guanine are a type of nitrogenous base called a purine, and contain a double-ring structure. Thymine and cytosine are a type of nitrogenous base called a pyrimidine, and contain a single-ring structure. Two scientists, James D. Watson and Francis H.C. Crick, spent a good amount of time devoted to determining the structure of DNA. Their efforts paid off, and they were the ones given credit for realizing that DNA was arranged in what they termed a double helix composed of two strands of nucleotides held together by hydrogen bonds. They noted that adenine always pairs with thymine (A—T) held together by two hydrogen bonds and that guanine always pairs with cytosine (C—G) held together by three hydrogen bonds. Each strand of DNA consists of a sugar-phosphate backbone that keeps the nucleotides connected with the strand. The sugar is deoxyribose. (See Figure 11.1 for a rough sketch of what purine-pyrimidine bonds look like.)

One last structural note about DNA that can be confusing is that DNA has something called a 5' end and a 3' end (Figure 11.2). The two strands of a DNA molecule run antiparallel to each other; the 5' end of one molecule is paired with the 3' end of the other molecule, and vice versa.

Replication of DNA

Human cells do not have copy machines to do the dirty work for them. Instead, they use a system called DNA replication to copy DNA molecules from cell to cell. As we discussed in Chapter 9, this process occurs during the S-phase of the cell cycle to ensure that every cell produced during mitosis or meiosis receives the proper amount of DNA.

The mechanism for DNA replication was the source of much debate in the mid-1900s. Some argued that it occurred in what was called a "conservative" (conservative DNA replication) fashion. In this model, the original double helix of DNA does not change at all; it is as if the DNA is placed on a copy machine and an exact duplicate is made. DNA from the parent appears in only one of the two daughter cells. A different model called the semiconservative DNA replication model agrees that the original DNA molecule serves as the template but proposes that before it is copied, the DNA unzips, with each single strand serving as a template for the creation of a new double strand. One strand of DNA from the parent goes to one daughter cell, and the second parent strand to the second daughter cell. A third model, the dispersive DNA replication model, suggested that every daughter strand contains some parental DNA, but it is dispersed among pieces of DNA not of parental origin. Figure 11.3 is a simplistic sketch showing these three main theories. Watson and Crick would not be pleased to see that I did not draw the DNA as a double helix … but as long as you realize this is not how the DNA truly looks, the figure serves its purpose.

An experiment performed in the 1950s by Meselson and Stahl helped select a winner in the debate about replication mechanisms. The experimenters grew bacteria in a medium containing ¹⁵N (a heavier—than—normal form of nitrogen) to create DNA that was denser than normal. The DNA was denser because the bacteria picked up the ¹⁵N and incorporated it into their DNA. The bacteria were then transferred to a medium containing normal ¹⁴N nitrogen. The DNA was allowed to replicate and produced DNA that was half ¹⁵N and half ¹⁴N. When the first generation of offspring replicated to form the second generation of offspring, the new DNA produced was of two types—one type that had half ¹⁵N and half ¹⁴N, and another type that was completely ¹⁴N DNA. This gave a hands—down victory to the semi—conservative theory of DNA replication. Let's take a look at the mechanism of semi—conservative DNA replication.

During the S-phase of the cell cycle, the double—stranded DNA unzips and prepares to replicate. An enzyme called helicase unzips the DNA just like a jacket, breaking the hydrogen bonds between the nucleotides and producing the replication fork. Each strand then functions as a template for production of a new double—stranded DNA molecule. Specific regions along each DNA strand serve as primer sites that signal where replication should originate. Primase binds to the primer, and DNA polymerase, the superstar enzyme of this process, attaches to the primer region and adds nucleotides to the growing DNA chain in a 5'-to-3' direction. DNA polymerase is restricted in that it can only add nucleotides to the 3' end of a parent strand. This creates a problem because, as you can see in Figure 11.4, this means that only one of the strands can be produced in a continuous fashion. This continuous strand is known as the leading strand. The other strand is affectionately known as the lagging strand. You will notice that in the third step of the process in Figure 11.4, the lagging strand consists of tiny pieces called Okazaki fragments, which are later connected by an enzyme called DNA ligase to produce the completed double-stranded daughter DNA molecule. This is the semi—conservative model of DNA replication.

Unliek my worck, DNA replication is not a perfect process—mistakes are made. A series of proofreading enzymes function to make sure that the DNA is properly replicated each time. During the first runthrough, it is estimated that a nucleotide mismatch is made during replication in one out of every 10,000 basepairs. The proofreaders must do a pretty good job since a mismatch error in replication occurs in only one out of every billion nucleotides replicated. DNA polymerase proofreads the newly added base right after it is added on to make sure that it is the correct match. Repair is easy—the polymerase simply removes the incorrect nucleotide, and adds the proper one in its place. This process is known as mismatch repair. Another repair mechanism is excision repair, in which a section of DNA containing an error is cut out and the gap is filled in by DNA polymerase. There are other proteins that assist in the repair process, but their identities are not of major importance. Just be aware that DNA repair exists and is a very efficient process. Here is a short list of mutation types that you should know:

1. Frameshift mutations. Deletion or addition of DNA nucleotides that does not add or remove a multiple of three nucleotides. mRNA is produced on a DNA template and is read in bunches of three called codons, which tell the protein synthesis machinery which amino acid to add to the growing protein chain. If the mRNA reads: THE FAT CAT ATE HER HAT, and the F is removed because of an error somewhere, the frame has now shifted to read THE ATC ATA THE ERH AT … (gibberish). This kind of mutation usually produces a nonfunctional protein unless it occurs late in protein production.
2. Missense mutation. Substitution of the wrong nucleotides into the DNA sequence. These substitutions still result in the addition of amino acids to the growing protein chain during translation, but they can sometimes lead to the addition of incorrect amino acids to the chain. It could cause no problem at all, or it could cause a big problem as in sickle cell anemia, a single amino acid error caused by a substitution mutation leads to a disease that wreaks havoc on the body as a whole.
3. Nonsense mutation. Substitution of the wrong nucleotides into the DNA sequence. These substitutions lead to premature stoppage of protein synthesis by the early placement of a stop codon, which tells the protein synthesis machinery to grind to a halt. The stop codons are UAA, UAG, and UGA. This type of mutation usually leads to a nonfunctional protein.
4. Thymine dimers. Result of too much exposure to UV (ultraviolet) light. Thymine nucleotides located adjacent to one another on the DNA strand bind together when this exposure occurs. This can negatively affect replication of DNA and help cause further mutations.