Tinkering with DNA

Simulating Molecular Evolution with Velcro

DNA is at the heart of biological evolution.  How does DNA change in ways that lead to the evolution of  so many wonderful creatures?  In this activity, you can tinker with simulated DNA to find out.

How did the tremendous variety of life on Earth arise? One of the greatest challenges to understanding evolution is in understanding how genetic variety emerged.  In the past, people believed that  errors in single nucleotides, known as random mutations, were the cause of most genetic variation.

For many people, it seemed improbable that the diversity of life could emerge from random point mutations. As it turns out, this intuition is correct. Point mutations necessary, but they are only a small part of the story.

We now know that the  mobile DNA plays a huge part in creating this genetic variety. Thanks to data from the sequencing entrie genomes, scientists have discovered that most of the genomes of eukaryotic organisms comes from “Mobile DNA” aka “jumping genes.

Mobile DNA drives evolution

Duplications, gene transfer and rearrangements of long stretches of DNA are what create big changes in the genome and in the organism.   This “mobile DNA”  or “jumping genes” creates the genetic diversity that allows for the evolution of organisms as diverse as giraffes, humans and manta rays. The Nobel-prize winning French biologist François Jacob called this process of duplication, moving, and subsequent modification “evolution by molecular tinkering.”

Summary: Students will create a model of a DNA genome using Velcro.  Students will use this model to demonstrate mobile DNA and the role of gene duplication and modification in evolution.  Students will move sections of “DNA” around the genome to simulate “jumping genes.”  Jumping genes, also known as mobile DNA, are an important source of genetic variation.  In creating genetic variation, mobile DNA is as important as point mutations, the more familiar concept of how DNA changes over time.

Grade level: 7-16

Time:  50 minutes

National Science Standards

•        9-12: This activity directly addresses two of the major six content standards for life sciences education in grades 9-12: Molecular basis of heredity and Biological evolution.  Following is pertinent text from the National Science Education Standards of the National Research Council:

THE MOLECULAR BASIS OF HEREDITY

  • In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes (as a string of molecular “letters”) and replicated (by a templating mechanism). Each DNA molecule in a cell forms a single chromosome. [See Content Standard B (grades 9-12)]
  • Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism’s offspring.

BIOLOGICAL EVOLUTION

  • Species evolve over time. Evolution is the consequence of the interactions of (1) the potential for a species to increase its numbers, (2) the genetic variability of offspring due to mutation and recombination of genes, (3) a finite supply of the resources required for life, and (4) the ensuing selection by the environment of those offspring better able to survive and leave offspring. [See Unifying Concepts and Processes]
  • The great diversity of organisms is the result of more than 3.5 billion years of evolution that has filled every available niche with life forms.
  • Natural selection and its evolutionary consequences provide a scientific explanation for the fossil record of ancient life forms, as well as for the striking molecular similarities observed among the diverse species of living organisms.
  • The millions of different species of plants, animals, and microorganisms that live on earth today are related by descent from common ancestors.
  • Biological classifications are based on how organisms are related. Organisms are classified into a hierarchy of groups and subgroups based on similarities which reflect their evolutionary relationships. Species is the most fundamental unit of classification.

Materials:

  • Double-sided Velcro strips in variety of colors – “Velcro One Wrap” packs with multiple colors are available from carft and office supply stores (about $4 a pack) (available on the web at: http://bevfabriccrafts.stores.yahoo.net/velcro15.html). Cut off the ends.
  • Roll of double-sided Black Velcro strips and white Velcro strips

Procedure: 

Cut off the ends of One-Wrap Velcro to create uniform widths of Velcro. In this activity, Velcro strips represent long stretches of DNA.  Each different color represents a different gene or DNA sequence.

As an advanced option, black Velcro may be used to represent non-coding regions and so-called “junk” DNA and the white Velcro used to represent regulatory regions of DNA.

1)  Assemble the “genome”

Stick together the ends of various colors of Velcro to represent the various genes that together form the genome.   The colorful bits of Velcro represent coding areas.  Black velcro may be used for non-coding DNA.

Option 1: Have students each place a gene and read the corresponding script that describes that particular gene and its product.

Option 2: You may use white strips of Velcro to represent the control regions of DNA. (In mammals, control regions account for up to 5% of the genome). You may also include large lengths of black Velcro to represent the 95% of the non-coding areas of the human chromosome. (note: bacterial genomes have little non-coding DNA)

2) Simulate a Point Mutation

Put a small sliver of velcro on one of the “genes” to simulation a single base pair change. For example, a point mutation in the hemoglobin gene from an A to T of the results in a change of protein structure. In this case, valine substitutes for glutamic acid. The result is that normal, disc-shaped red blood cells turn to a sicle shape. There is a benefit to this mutation in that

3) Simulate a Deletion

Remove a Velcro strip from the genome (in above photo, the blue “gene” was removed ).  This is an example of deletion.  If this gene was important for survival, the cell in which this mutation occurred will not survive. If this mutation was deleterious and in a sperm or an egg cell, the resulting offspring will not survive.

4) Simulate an Insertion

a) Take the blue Velcro strip you removed and insert it in a new place on the genome (in this photo, an orange gene was inserted between the green genes.)

b) Note that sometimes insertions occur in the middle of another gene, which inactivates that gene. One real life example of this is an insertion of a sequence called Alu in the NF-1 gene, thereby causes neurofibromatosis.

5) Simulate a Duplication

“Gene duplications are a common form of change in DNA.” ~ Sean Carroll in “Making of the Fittest.

Simulate the Light Detecting Gene Opsin

How does color vision evolve? Is it possible that a thing as complex system as the human eye could evolve only by a series of random point mutations?

 

Other Gene Duplications

Another famous example of gene duplication is found in the oxygen-carrying enzyme hemoglobin genes in humans and many other creatures. Humans have several hemoglobin genes, some of which function at different stages in human development.

New Function Sometimes the copied DNA is recruited to perform an entirely new function. (ref) The DNA may be modified through subsequent point mutations to provide another function in the organism.  An example of this is the heat-shock proteins and other metabolic proteins which have been duplicated and modified to serve as the clear crystalin protein in the lens of eye (ref).

5b) Simulate Jumping Junk Genes

Over 90 percent of the human genome is made of non-coding and non-regulatory DNA. This is the dark matter of DNA. Why is this dark DNA here? Much of it is the result of jumping genes, like a transposable element called the Alu sequence (mentioned above).  Found only in primates, this 300 base pair sequence is repeated about one million times and makes up about 10% of the human genome, accounting for a significant part of the non-coding “dark matter” of the genome. For this simulation, take a piece of black velcro, duplicate it many times, and have it jump all over your growing chromosome.

6) Simulate Gene Transfer

DNA often moves from one organism to another.  This can happen when we are infected with viruses. Sometimes the virus leaves behind a bit of itself in the host genome.

7) Simulate Interspecies Gene Transfer

Sometimes, DNA move from one species to another.  This is an important source of raw material for evolution.  This has practical implications.  For example, Bird Flu DNA hops from one species of bird to another and eventually into humans. This novel DNA poses a threat to our immune systems.

In early evolutionary history and for bacterial evolution today, interspecies gene transfer is an important process for creating novelty. (see references to Woese, 2002 and Margulis 2003 below)

  • Viruses
  • Transposable Elements
  • Symbiosis as a source of inherited variation

8) Simulate Recombination

During meiosis, entire stretches of DNA from one chromosome recombine with DNA from another chromosome.

 

Jumping Genes and Mobile DNA

Mobile DNA is the biggest driver of biological evolution.

Barbara McClintock won a Nobel prise for showing how transposons move around the genome of corn. Since this great discovery, we now know of retrotranposons, which account for over half of some genomes!!!!

Transposons are just one way that DNA moves around.  Viruses move DNA between species.  In bacteria, interspecies gene transfer is happens all the time and is most clearly seen today in the evolution of  antibiotic resistent bacteria.  In eukaryotes, one of the great evolutionary traits was that of recombination during meiosis.  This emergent ability allows cells to move DNA more rapidly than ever before.

We see evidence of mobile DNA everywhere.  In humans, over 10% of our DNA is made up of just this one type of mobile DNA called Alu elements.  These  Alu sequences are approximately 350 base pairs long and do not contain any coding sequences.  Each human genome contains about 1,500,000 copies of the Alu sequence.