DNA Components, Structure and Replication

Teacher Guide


Notes for the teacher.

This exercise is to help students learn DNA structure and replication through exploration. It can also be used to reinforce these concepts following lecture. It is not designed to compare DNA to RNA although you could easily alter this exercise to explore that.

Answers are given in italics throughout the exercise.

Part I - Components of DNA
I usually ask the students to read through themselves, then I go over the answers with them as a class.

Part II - Structure of DNA
The students try to fit pieces together to make the second strand of DNA. This must be done with some care! Students be sure that the hydrogen bonds line up. Also, the integrity of the sugar phosphate backbone must be maintained (ie - bases at odd angles that would break the regularity of the backbone are not allowed).

The bases for this exercise can be created by cutting apart the piece of DNA provided at the end of this teacher guide. It is helpful to cut all the bases apart in a similar manner.

Part III - DNA Synthesis
I first ask the class together what they think the meaning of the words are in English. Alternatively you can have them work in small groups to do this, or to look up the words in the dictionary if they don't know. I then work with the students as a class or in groups to help them propose for definitions relevant for DNA synthesis. This may require some "coaching."

I then have the students explore DNA synthesis and try to come up with themselves, the steps that are involved based on what they know about DNA structure, the definitions they just developed, and the pieces they are supplied with. Again, this may require some "coaching." The goal is for students to learn through exploration.

The pieces for this exercise can be created by cutting apart the piece of DNA provided at the end of this teacher guide. Note that you will need to cut out both individual bases, plus the appropriate primer. The answer key is drawn showing GCACG as a primer, but you may choose a different primer if you wish.



Part I - Components of DNA - DNA is made of three types of compounds

1 — Phosphate groups which are negatively charged and give DNA molecules a negative charge.

2 — A 5 carbon sugar, deoxyribose (hence the name deoxyribonucleic acid). There are two sugars found in nucleic acids; ribose is found in RNA (ribonucleic acid) and deoxyribose in DNA. Deoxyribose refers to the fact that one of the hydroxyl (OH) groups is missing from this sugar.

Examine the two sugars below. Identify which is ribose and which is deoxyribose.



Deoxyribose Ribose

Note that the carbons in deoxyribose are numbered 1 through 5. In deoxyribose, which carbon is missing the OH group?

2’

 

3 Nitrogen bases — Four different nitrogen bases are found in DNA. They are adenine (A), cytosine (C), guanine (G) and thymine (T). Their structures are shown below.



Part II - Structure of DNA

1. Examine the chain of bases on the next page. Note that the deoxyribose sugar and phosphates are linked together to form a backbone. Which two carbons in a deoxyribose molecule are linked to a phosphate? (note that the carbons in deoxyribose are numbered).

3’ and 5’

 

2. DNA is double stranded (ds), meaning there are two of the above strands together. Try to assemble a ds DNA molecule with sugar phosphate backbones on the outside, and nitrogen bases on the inside. Use the chain of bases on the next page as one strand, use the loose bases provided to form the other strand. Note that the hydrogen bonds, represented by the dotted lines, must line up. Also, the bases must fit in a way such that a continuous strand is formed.

This must be done with some care! Students be sure that the hydrogen bonds line up. Also, the integrity of the sugar phosphate backbone must be maintained (ie - bases at odd angles that would break the regularity of the backbone are not allowed).

 

3. Observe your DNA molecule

What bases always pair together? (i.e., what base is always found paired with A?, with C?, G?, T?) Two bases that are always found across from each other are said to be complementary to each other.

A with T, 2 hydrogen bonds

G with C, 3 hydrogen bonds

 

4. Now look at the deoxyribose molecules in the two separate strands. What can you say about the orientation (direction) of the two strands with respect to each other?

They run in opposite directions with respect to one another.

 

5. Which end of each strand of DNA would you call the 5’ end?, the 3’end? Label these on your assembled ds DNA molecule (each of the two strands of DNA will have one 5’ end and one 3’end).

 

 

6. Experiment with your ds DNA molecule.

Can you form a continuous ds molecule with all the sugars and phosphates linking up if you mispair the bases? (say an A with an A etc?)

No

7. Can you do it if you have the two strands in the same direction?

No

 



Part III — DNA Synthesis

Define the meaning of the following three words in everyday English.

Primer

A coat of paint applied before the real coat.
A mechanism to help start a lawn mower etc
Something used to prepare for use or action

Template

A pattern or frame used to make a copy of something

 

Polymerize

To link or become linked together in long chains

 

Remembering that enzymes end in "ase" — describe in everyday English what you think DNA polymerase is.

An enzyme which polymerizes DNA.

 

DNA polymerase is the enzyme which adds single bases (A,C,G,T) to the growing chain. Note that DNA polymerase must follow three rules

1. It can only add bases to a reaction which is already started

2. It can only add a base across from an existing base

3. It will only add the base which is complementary to the existing base

Given these three rules that DNA polymerase must follow, propose a definition for the following two words which could have a relevance for DNA synthesis.

Primer

Something that starts the polymerization reaction for synthesis of DNA

 

Template

Something from which the new DNA is copied

Below is a list of items needed for a cell to synthesize DNA (or for a scientist to synthesize DNA in a test tube using a biological reaction).

1. DNA template — DNA strand to be copied

2. DNA polymerase — You will play the role of this enzyme which adds single bases (A,C,G,T) to the growing chain. Remember, as DNA polymerase you can only add a base to a 3’OH group (review the first page of this handout) and you can only add the base which is complementary to the base across from it on the template.

3. Primer — a short piece of DNA complementary to the template strand. It starts the DNA synthesis reaction by providing a 3’OH group to which DNA polymerase can add the next base.

4. A,C,G,T — bases which are added by DNA polymerase to the growing DNA strand.

Look at the items needed (pieces have been supplied so you can experiment with them) and their functions. Remember you will play the role of DNA polymerase. Propose a mechanism by which DNA is synthesized — do this in one of the three following ways

 

Template 5’ A A C T G C C A A C G T G C 3’

Primer 5’ G C A C G 3’

  1. Primer binds to template DNA strand. This binding is specific and occurs between complimentary bases in the template and primer.
  2. 5’ G C A C G 3’
    3’ C G T G C A A C C G T C A A 5’

  3. DNA polymerase sequentially adds bases to the 3’ end of the growing chain.

5’ G C A C G T 3’
3’ C G T G C A A C C G T C A A 5’

5’ G C A C G T T 3’
3’ C G T G C A A C C G T C A A 5’

5’ G C A C G T T G 3’
3’ C G T G C A A C C G T C A A 5’

3. DNA polymerase adds the base which is complimentary to the template strand.

 

In which direction is the growing DNA strand synthesized? 5’ to 3’ or 3’ to 5’?

5’ to 3’

 

 



Each base in the figure below may be cut out in order to complementary base pair with the chain of bases in Part II-Structure of DNA.



Each base in the figure below may be cut out in order to complementary base pair with the chain of bases in Part III-DNA Synthesis.