DNA Beads

Beads On Pipecleaners to Simulate DNA Replication, Transcription and Translation



Hands on Activitiy by Cathy Russell.

 “At the heart of evolution – at least on this planet – is a string-shaped molecule called deoxyribonucleic acid.”
~ Carl Zimmer in The Virus and the Whale

Summary: Students will “synthesize” a model of DNA using colorful beads and pipe cleaners.  They will then “transcribe” this DNA into messenger RNA and then “translate” this into a protein.

Grade level: 4-12

Time: Best in two  or three class periods, depending on the age of student

Student Learning Outcomes:

  • Students will be able to demonstrate how information is stored in base pairs of the DNA molecule
  • Students will be able to demonstrate how the information from DNA is transcribed into RNA and translated into proteins.
  • Students will demonstrate how point mutations can alter DNA and subsequently proteins.
  • Students will be able to tell how changes in DNA affect evolution.
  • Students will be able to discuss the usefulness and limitations of this model.

Introduction:

DNA is the information storage molecule of life.  Comparing DNA sequences shows the relatedness of all living creatures.  Evolution works through the modification of DNA, so to properly understand biological evolution, it is helpful to understand the basic structure of DNA. In this activity we will make a model of a gene. In this case, it will be the gene encoding oxytocin, a small polypeptide that works as a hormone in mammals (see background below).  We use this sequence because it is small and relevant in people’s lives.

This activity uses beads and pipe cleaners, which are inexpensive, readily available and easy to assemble.

Materials

Per student:

  • Coloring page demonstrating base pairing (optional)
  • 2 black pipe cleaners to represent DNA
  • 1 red pipe cleaner to represent RNA
  • 1 blue pipe cleaner to represent protein
  • Beads in the following colors:
    • B=blue = adenine
    • G=green = thymine
    • Y=yellow = guanine
    • R=red = cytosine
    • L = black = uracil
  • Multicolored and shaped assortment of 20 different types of beads to represent amino acids.

If you can get them, Pop Beads in the various colors are ideal for creating models of DNA.  However, they are more expensive and not as readily available.

 

Notes to Instructor:  This is a simplified demonstration of DNA replication, transcription and translation. The hundreds of enzymes, molecules, and other details of DNA replication, transcription and translation can overwhelm a student with detail that can diverge their attention from the main function of DNA, which is information storage.  In this exercise, the focus is on the overview of DNA structure with emphasis placed on the flow of information from DNA to RNA to protein and how this relates to evolution.

Even though the models presented are simplified, it would be helpful for the teacher to have a deeper understanding of the process to answer student’s inevitable questions. A clear and thorough explanation of DNA is in the text book, Biology, by Neil Campbell, Jane B. Reese, and Lawrence G. Mitchell. This outstanding college biology textbook is permeated with great information on DNA and evolution.

It has been said “all models are wrong, some models are useful.”  Like all models, the model presented here is an oversimplification and there exist possibilities for students to get wrong ideas. As with the use of all models, it’s important for students to understand the strengths and limitations of the model, so that the student doesn’t confuse an artifact of the model with what the model is trying to represent.

Directions:

Set Up:

First, make a strand of DNA.  Put red, yellow, blue and green beads on a black pipe cleaner corresponding to the DNA sequence below:

DNA Sequence: T-C-T-T-G-G-A-T-T-C-A-A-A-A-T-T-C-T-C-C-C-C-T-C-C-A-A

Color Code:   G-R-G-G-Y-Y-B-G-G-R-B-B-B-B-G-G-R-G-R-R-R-R-G-R-R-B-B

Each bead color corresponds to a different nucleotide as follows:

  • B=blue = adenine
  • G=green = thymine
  • Y=yellow = guanine
  • R=red = cytosine

Synthesize DNA:

When new cells are made, DNA is replicated and a copy is given to each new cell.  In this activity, imagine that you are DNA polymerase, the enzyme that makes DNA using a DNA template.

Now imagine that the double stranded DNA helix was already unwound, and you are working with only one strand of the DNA,  Put beads on another pipe cleaner that complement, or create base pairs, with the sequence of beads on the first pipe cleaner.  Wherever there is a cytocine (red bead), compliment it with a guanine (yellow bead.)  And where there is am adenine (blue bead,) compliment it with a thymine (green bead.)

Once you have added nucleotides to complement the original strand of DNA, create a double helix by twisting the two strands together.  In the cell, the complementary base pairs stick together with hydrogen bonds.  In the case of the C and G  bond, there are 3 hydrogen bonds. In the case of AT, two hydrogen bonds.  The DNA is going in opposite directions. DNA usually has 10 nucleotides per turn.

 

Discussion and Questions:

  • Did anyone accidentally put the wrong bead on the pipe cleaner?
  • This is a mutation. If the mutation remains, what will happen to the mRNA and protein?
  • How does this affect evolution?
  • If the mutation happens in a somatic cell, it will not affect evolution.  But if it happens in a sperm or an egg cell, this change will be passed on to the next generation.
  • What are some analogies of nucleotides?  Letters of the alphabet? Computer code?

Discuss the limitations of this model with your students.

  • One obvious difference is that new DNA is assembled from individual units to create the backbone strand.  In this model, we’re using a pipe cleaner to hold the “nucleotide” beads in place.
  • In the cell, DNA is double stranded and must first be unwound. In this bead model, no DNA gyrase was used to open up the double strand, as happens in cells.
  • DNA polymerase must have a “primer,” that is, a strand of nucleotides from which to add more nucleotides.  In our model, we do not use a primer, which in eukaryotic cells is a short sequence of RNA.

Transcribe to RNA

Encourage students to imagine that they are RNA polymerase, an enzyme that uses a DNA template to make messenger RNA.

Unwind the double strand of DNA that you made.

Take a red pipe cleaner and line it up with the black DNA.

Now add beads to the pipe cleaner that complement the beads on the DNA. This process is much the same as synthesizing DNA, except instead of a thymine, a uracil is used instead to complement adenosine. Use the code as follows.

UCU—UGG—AUU—CAA—AAU—UCU—CCC—CUC—CAA– NH2

LRL—LYY—BLL—RBB—BBL—LRL—RRR—RLR—RBB—NH2

  • B=blue = adenine
  • Y=yellow = guanine
  • R=red = cytosine
  • L = black = uracil

Note that only one strand is the “sense” strand.  The RNA polymerase would recognize this strand because it is the one with the promotor, a sequence of DNA recognized by the RNA polymerase.  (which, for simplicity, we have not included.)

Translate to Proteins

 

Translation is the process of converting information from the mRNA into protein.  Take the red beaded mRNA strand and imagine that it goes to a ribosome, a cellular “machine” that uses the mRNA template to create a protein.

In translastion, the ribosome reads 3 nucleotides as a “codon” that corresponds to an amino acid.  To simulate the creation of a polypeptide, put one bead on a blue pipecleaner.   In this example, the

 

Amino Acid Sequence

Cys  -Tyr  -Ile  -Gln  -Asn  -Cys  -Pro-  Leu-  Gly

RNA Sequence (followed by color code)

UCU—UGG—AUU—CAA—AAU—UCU—CCC—CUC—CAA

LRL—LYY—BLL—RBB—BBL—LRL—RRR—RLR—RBB

  • B=blue = adenine
  • G=green = thymine
  • Y=yellow = guanine
  • R=red = cytosine
  • L = black = uracil

In this simplified activitiy, we have not used a start codon (AUG) that the ribosome recognizes to begin translation.

Discussion:

DNA is shared by all organisms. Although details vary, all organisms replicate their DNA, transcribe it into RNA and translate mRNA into proteins.

Can you think of examples of point mutations affects people?

Classic is sickle-cell anemia.

Background:

Oxytocin

Oxytocin is sometimes called the “love hormone”  because it induces feelings of connection and well-being in people. Found in mammals, this hormone is involved in bonding and trust between people.  In humans it was first discovered to be released mainly during the let-down response of lactation and in the distention of the vagina, which facilitates birth.

Amino Acid Sequence

Cys  -Tyr  -Ile  -Gln  -Asn  -Cys  -Pro-  Leu-  Gly  -NH2.

RNA Sequence (followed by color code)

UCU—UGG—AUU—CAA—AAU—UCU—CCC—CUC—CAA

LRL—LYY—BLL—RBB—BBL—LRL—RRR—RLR—RBB

  • B=blue = adenine
  • G=green = thymine
  • Y=yellow = guanine
  • R=red = cytosine
  • L = black = uracil

Factoids:

  • Each human cell contains about two meters of DNA.  5 cm per chromosome x 46 chromosomes  = 230 cm = 2.3 meters.
  • Human body contains around 100 trillion cells.
  • Humans have around 25  trillion red blood cells
  • Cells with DNA = All cells – red blood cells = 75 trillion cells
  • Human body has 2.3 meters/cell x 75 trillion cells =  That equals about 172  billion kilometers.
  • The distance to the sun and back is about 300 million kilometers.
  • If stretched from end to end, DNA from our bodies would goto the sun and back 172 billion /300 million kilometers,  almost 575 times!

Resources:

Biology by Neil Campbell, Jane B. Reese, and Lawrence G. Mitchell. This outstanding biology textbook for college students is permeated with great information on DNA and evolution.

DNA Learning Center – comprehensive web site with lots of information of DNA.  The Romanov Mystery is http://www.dnalc.org/home.html

Genetic Origins:” The Study of human evolution begins with your DNA. http://www.geneticorigins.org/geneticorigins/

This  site provides biochemical methods and computer tools to allow students  to use their own DNA “fingerprints” as a starting point in the study  of human evolution. Two experiments are currently available, which  are supported  by reagents and ready-to-use kits available from Carolina Biological  Supply Company.

National Genographic – “we are all related—descended from a common African ancestor who lived only 60,000 years ago.” https://www3.nationalgeographic.com/genographic/
National Standards Addressed (NRC):

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.