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Topics in Depth

The Theme of Common Mistakes in DNA Structure, Replication, and Technology

The Genetic Code

Many people confuse DNA with RNA, which is why TV networks canceled their buddy cop drama. A few easy ways to tell the difference are as follows:

  • DNA has no 2' hydroxyl, which is why it is called "deoxy" ribonucleic acid. See what they did there?
     
  • DNA is rarely single stranded, while RNA is regularly single stranded.
     
  • DNA has thymine, but RNA has uracil.
     
  • DNA is found as a double helix, while RNA forms structures from base-pairing within the RNA molecule.
     

Often, when people are trying to read a sequence of DNA, they are unaware that there are two strands: a positive strand that goes from 5' to 3' and a minus strand that goes 3' to 5'. It is important to realize that sequences are always read 5' to 3'. Therefore, if the sequence in question is from the minus strand, you would need to reverse it to know the correct order for the positive strand.

DNA Packaging

How DNA is packaged can be confusing. Acetyltransferase? Methylwhosiwhatsis? Enzymes are straightforward to understand if you break them down:

  • Acetyltransferase = Acetyl + Transfer + Ase
      
    Acetyl is a negatively charged group, transfer means "add to," and –ase is a general suffix added to all enzymes. This enzyme (acetyltransferase) adds an acetyl group to histones. We feel like Sylvester the Cat. Sufferin succotash!
      
  • Methyltransferase = Methyl + Transfer + Ase
      
    Methyl is a hydrophobic group, and the same as above for the rest of the word. Therefore, this enzyme adds a methyl group.
     
  • Deacetylase = De + Acetyl + Ase
     
    "De" means to "undo" the acetyl group. This enzyme removes acetyl groups.

From Genes to Proteins

One of the biggest confusions about transcription and translation arises from keeping track of what strand of nucleotide sequence is being used for what. The mRNA transcript is identical in sequence to the gene sequence in the DNA. Therefore, the template for mRNA is the complementary strand of DNA, which is identical in sequence to the anticodon sequence that the tRNA binds to.

Nucleotide TypeSequence
Gene (DNA)GTAGTCTTGACTGAC
mRNAGUAGUCUUGACUGAC
Template for mRNAGTCAGTCAAGACTAG
AnticodonsGUC, AGU, CAA, GAC, and UAG

Many people find translation and transcription confusing, but it is actually straightforward if you think about the roots of the words. Transcription comes from "transcribe," which essentially means to rewrite something. Court reporters are transcribers: they copy what is said aloud onto paper. Transcription in a cell is copying the gene sequence in DNA to RNA. Nucleotides are copied into nucleotides.

However, translation comes from "translate," which suggests the action that RNA information is translated into protein information through amino acids.

DNA Replication

One of the major misconceptions of DNA replication and cell division is the role of "interphase" in cell replication. Most people think that interphase is this inert "sleeping" phase, and all the exciting activity happens in mitosis. Yet again, it is those mitosis-centric jerks that keep maligning "interphase."

As mentioned before, interphase is where the cell prepares for another round of mitosis, turning on metabolic processes (G1), activating DNA replication (S), and preparing the infrastructure of microtubules for mitosis/meiosis to occur (G2). Therefore, even though it is not as exciting as mitosis, it is still a lot of work. Would it be correct to say that the cell spends most of its time in interphase?

Polymerase Chain Reactions

One of the biggest problems with PCR is proper primer design. If you wanted to amplify a gene of interest, you need to select primers that match the gene properly. Therefore, you need to make a 5' primer that is identical to the start of the gene, and a 3' primer that is identical in sequence to the reverse complement of the 3' end of the gene. If we take the example from Robertson and Phillips (CITATION) below showing the aroA gene:

We want to amplify the underlined sequence, so we will design primers that will match the grey sequence. Therefore, our 5' primer will be: 5'-GGAAGGGAGTGGTGAAGAG-3', and our 3' primer will be: 5'-CTGCAAAGAACCATCAGGC-3'. Notice that the 3' primer is the reverse complement of the 2nd grey sequence, while the 5' primer is identical to the 1st grey sequence.

Genomes

Many people think of their genomes as containing only genetic information. There are a lot of DNA sequences that do not have a function, or have functions that we do not know of yet. The name "junk DNA" is often applied to these DNA sequences; however, it is unclear whether these sequences are actually "junk," or if they serve a function that we have yet to understand. Intronic sequences sometimes have promoters that encode mRNAs that are antisense to the RNAs that regulate mRNA expression. Antisense RNAs bind sense mRNAs to destroy the mRNAs. The flanking sequence also encodes the enhancer sequence that affects activation of gene expression. And, sometimes, the distance of the enhancer sequence is important for expression, so it remains unclear whether these can be considered "junk," either. In the words of our mom, all bases are special because they make us who we are.

Recombinant DNA

Hopefully, you do not come out of this unit thinking there is a SUPER APE gene, because there is not. Beyond that, many people are concerned about the use of recombinant DNA, though most of these concerns are unwarranted. In many instances, especially for crops, genetic engineering is not too dissimilar to what has already been going on for years by cross-breeding plants, like Mendel's work. Recombinant DNA has sped up the process in many instances. Though, in some instances, genetic engineers have inserted genes that never could be introduced naturally, like tomatoes with fish genes.

Many of the fears of using biotechnology come from human conventions of what is "natural." Putting pig hearts in humans sounds terrible unless you need a heart transplant. Because much of the technology is in its infancy, the failures of biotechnology are always overpublicized compared to the successes. That being said, there should also be more caution when introducing genetically modified products for general usage: they must be properly tested beforehand to confirm that they cause no detrimental effects to the health of humans, the environment, or the planet at large.

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