Class Calendar

November 25/26

Science 8/10

Please contact Mr.Wenzel for more information.

Biology 12

Homework: Finish question sheet

Homework: Please select a SHORT article or story about genetic engineering, gene therapy or a genetic disorder involving proteins (ex. Cystic Fibrosis). And e-mail it to my e-mail address by December 4th.

Check out Scientific American, Discover, BBC, CBC, etc...

Page 1 of DNA SECTION in Journals

Students should be able to answer the following questions...

1. Describe the structure and function of DNA
2. Describe the three steps in the semi-conservative replication of DNA

  • unzipping (DNA helicase)
  • complimentary base pairing (DNA polymerase)
  • joining of adjacent nucleotides (DNA polymerase)
3. Describe the purpose of DNA replication
4. Identify the site of DNA replication

Research Notes:

James Watson and Francis Crick worked out the 3D structure of DNA using molecular models made of wire
  • The molecule consists of 2 chains wound together in a spiral (i.e., a double helix).
  • The sides of the chains are made of alternating sugars and phosphates, like the sides of a rope ladder.
  • The ladder forms a twist every ten bases.
  • Pairs of nitrogenous bases, one from each strand, form the rungs of the ladder. In order for the ladder to have a uniform width, a small base must be paired with a large base. A pairs with T and C pairs with G. This is called complementary base pairing.
  • The two strands are held together by hydrogen bonding between bases.
  • Note that the chains have direction. Each strand has a 3’ end with a free OH group attached to deoxyribose and a 5’ end with a free phosphate (P) group attached to deoxyribose. This arrangement is called antiparallel.3. Replication of DNA
When a cell divides, the DNA must be doubled so that each daughter cell gets a complete copy. It is important for this process to be high fidelity because any errors made would be inherited by the offspring and these errors would tend to accumulate with each generation.

Because each strand is complementary to the other, each can form a template when separated. When a cell copies a DNA molecule, each strand serves as a template for ordering nucleotides into a new complementary strand. One at a time, nucleotides line up along the template strand according to the base-pairing rules.

An experiment in the late 1950s by Matthew Meselson and Franklin Stahl demonstrated
that replication was semiconservative.
  • The replication of a DNA molecule begins at special sites, origins of replication. A specific sequence of nucleotides marks the origin. (a sequence of about 150 nucleotides rich in GATC)
  • Humans have hundreds of origins from which replication proceeds on both strands in both directions.
  • At the origins, the DNA strands are separated, forming a replication “bubble” with replication forks at each end. An enzyme called helicase separates the strands.
  • Elongating a new strand
  • After the two strands are separated, DNA polymerase reads the bases on the template strand and attaches complementary bases to form a new strand. (DNA polymerase works at a rate of about 50 nucleotides per second)
  • DNA polymerase can only attach the 5' phosphate (P) of one nucleotide to the 3' hydroxyl (OH) of the previous nucleotide that is already part of a strand. The enzyme can only work by building a new strand in the 5' ΓΏ 3' direction.

Problem of antiparallel strands
  • Remember that the DNA molecule is arranged with the strands going in opposite directions so the 3' end of one strand is aligned with the 5' end of the other.
  • DNA polymerase adds nucleotides only to the 3' end but can only do this on one strand, the leading strand.
  • The other strand has a 5' P at the end rather than a 3' OH like DNA polymerase needs. This strand, the lagging strand, must be made in short fragments (Okazaki fragments) going in the direction opposite to the leading strand. Another enzyme, DNA ligase, then fills in the gaps by joining the fragments together. (fragments are 100-200 nucleotides in eukaryotes; 1000-2000 in prokaryotes)g. Priming DNA synthesis

  • DNA polymerases cannot initiate the synthesis of a new strand of DNA.
  • A short stretch of RNA (5-10 nucleotides) with an available 3’ end is built. This short piece is called a primer and is built by primase, a RNA polymerase.
  • After formation of the primer, DNA polymerase can add new nucleotides to the 3’end of the RNA primer.
  • The leading strand requires the formation of only a single primer as the replication fork continues to separate. For synthesis of the lagging strand, each Okazaki fragment must have its own primer.
  • Another DNA polymerase then replaces the RNA nucleotides of the primers with DNA nucleotides.
Replication error rate, DNA damage and repair

The active site of DNA polymerase must recognize all four nucleotides. This means that it is difficult to determine if a nucleotide is mistakenly in the active site. 

Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100,000 base pairs.

DNA polymerase checks for these errors by checking the width of the helix. The final error rate is only one per ten billion nucleotides.

Constant exposure to chemicals, viruses, and radiation also cause damage to DNA so human cells have about 130 enzymes which constantly check DNA for errors.