DNA Components, Structure and Replication


 

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.



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

 

 

 

3Nitrogen 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).

 

 

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.

 

 

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.

 

 

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?

 

 

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?)

 

 

 

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

 

 

 

 



Part III — DNA Synthesis

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

Primer

 

 

 

 

Template

 

 

 

 

Polymerize

 

 

 

 

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

 

 

 

 

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

 

 

 

 

Template

 

 

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

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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