Bowie- Biology 12 Understanding DNA Page 8 of 8

Bowie- Biology 12 Understanding DNA Page 8 of 8

DNA Notes

Name: ______Date: ______

·  DNA stands for deoxyribonucleic acid.

·  DNA is the hereditary material. It allows for the transfer of genetic material from parent cell to daughter cell and from parent organism to offspring.

·  The 3 main components of DNA are: a deoxyribose sugar, a phosphate group, and a nitrogenous base.

·  There are four nitrogenous bases in DNA. They include: Adenine (A), guanine (G) which are double ringed purines and thymine (T) and cytosine (C) which are single ringed pyrimidines. Uracil (U) is found in RNA in place of thymine.

·  DNA is made of polymers of many nucleotides held together by phosphodiester bonds between the phosphate group and the adjacent sugars.

·  Erwin Chargaff determined that Adenine and Thymine always pair with each other and Cytosine and Guanine always go together. This is called Chargaff's Rule.

·  Hydrogen bonds hold the nucleotide base pairs together. Three H-bonds join C and G while only 2 H-bonds join T and A.

Naming the Carbon locations on the sugar

·  Carbons are numbered clockwise, starting with the carbon atom to the immediate right of the oxygen atom.

·  The first one would be called 1' (pronounced 1 prime), the next would be 2' (2 prime)...

·  The nitrogenous base attaches to the sugar at the 1' location (via a glycosyl bond).

·  The phosphate group attaches to the sugar at the 5' location (via an ester bond).

The Race for the Structure of DNA

·  In the early 1050's, three teams of people were working to uncover the hidden structure of DNA.

·  Linus Pauling (a 2x Noble Prize Winner) was building ball and stick models using his expertise in chemistry. While he did propose 1 model, it did not answer the questions being asked nor did it show how copying of the DNA could occur. His son, Peter Pauling, went to work with another group in Cambridge, England.

·  Rosalind Franklin and Maurice Wilkins were both working at King's College in London doing studies using the diffractions seen with X-ray crystallography. Though their work was based on serious scientific evidence, they did not work together harmoniously and thus were not always working synergistically. Franklin eventually uncovered the shape of DNA when she found an x-ray diffraction in a cross pattern. Unfortunately, Wilkins shared this data with Watson who used it to further his own work.

·  James Watson and Francis Crick were considered lazy slackers who did not embrace the serious need for scientific experimentation and evidence. They focused on trying to determine the structure of DNA instead, using 3D modelling. Despite their less-than-scientific ways, they were asking all the right questions and when Wilkins showed the x-pattern of Franklin's x-ray diffraction, he immediately knew (thanks to Crick's instruction) what the structure might look like. They came up with the modern structure of DNA that accurately answered the question as to how DNA can create perfect copies of itself.

·  Watson, Crick and Wilkins won Noble Prizes for their Discovery of the structure of DNA. However, Franklin did not receive one as she died before the awards were given.

DNA Double Helix Structure

·  DNA is made of 2 antiparallel strands of nucleotides.

·  It is important to be able to identify the 3' and 5' ends of each strand.

·  Thanks to Chargaff's Rule, if you know the sequence of one of the strands, you can synthesis the opposite strands by always pairing T with A and C with G. By convention, we only state the 5' to 3' strand, since the complementary strand can be easily deduced.

5' - GCAATCTA - 3'

3' - CGTTAGAT - 5'

·  The most important aspect of Watson and Crick's DNA model was that it enabled us to understand how it could replicate identical copies of itself.

·  Replicating identical copies is necessary in order for single cells to be replaced as they age or are damaged. It also happens as embryos develop from single cell all the way through to adulthood. This process is known as mitosis.

DNA Replication

·  Initially scientists wanted to know exactly how the DNA strand would make a copy of itself.

·  There were a few possibilities:

·  Semiconservative: each DNA molecule is made of one parent strand and one newly synthesized strand.

·  Conservative: each DNA molecule reforms so that both new strands stay together and both parent strands stay together.

·  Dispersive: where bits and pieces of the parent and new strands are interspersed in both strands following the replication.

·  Experiments showed that the semiconservative model was correct while the other two were rejected.

The Process of DNA Replication

·  During replication the two DNA strands separate and serve as templates strands.

·  DNA replication begins at the origin of replication.

·  At the origin, the two strands of DNA unwind and DNA replication proceeds (following the AT/CG rule) outward from the origin in opposite directions. This is a process called bidirectional replication.

·  In simple bacteria, which have a small circular chromosome, there is a single origin of replication.

·  In more complex eukaryotes, with large, linear chromosomes, there are many origins of replication in order to allow complete replication to occur in a reasonable amount of time.

·  The origin of replication forms a bubble that creates two DNA replication forks.

·  Replication begins near the opening of each fork.

·  The building of the new DNA always begins with a primer.

·  New DNA is always built in the 5' to 3' direction.

·  The mechanism for building the two new daughter strands is very different.

·  One strand will be the leading strand. The other will be the lagging strand.

·  The leading strand moves in the same direction as the fork is moving.

·  The leading strand is replicated as one long continuous molecule.

·  The lagging strand is made in a series of small fragments which will eventually form a continuous strand. The synthesis of this strand goes in the direction away from the fork. These fragments are known as Okazaki fragments. (Named after Reiji and Tuneko Okazaki who discovered them in the late 1960's).

Proteins Needed for DNA Replication

Step 1: Formation and Movement of the Replication Fork

§  An origin or replication of where the strands begin to separate in order for replication to occur.

§  DNA helicase is an enzyme binds to one of the strands at the origin and travels in the 5' to 3' direction. It uses energy from ATP to keep the fork moving forward (away from the origin). The movement of the helicase causes additional coiling just ahead of the replication fork. To reduce this, another enzyme is needed.

§  DNA topoisomerase (also called DNA gyrase) alleviates the additional coiling above the replication fork.

§  Once the strands have been separated, they must be held apart to prevent them from rebinding annealing) until the complimentary daughter strands can be formed. This is done with the help of single-strand binding protein.

Proteins Needed for DNA Replication

Step 2: Synthesis of the Leading and Lagging Strands

§  In prokaryotes, there are 3- 5 enzymes that serve to replicate and repair the DNA strand. These are DNA polymerase I, II, III, IV & V.

§  In eukaryotes, there are 12+ DNA polymerases involved.

§  DNA polymerase is responsible for covalently linking nucleotides together to form DNA strands.

§  As DNA polymerase III slides along the DNA, free nucleotides with 3 phosphate groups, called deoxynucleoside triphosphates, hydrogen bond to the exposed bases in the template strand according to the AT/GC rule. DNA polymerase III breaks the bond between the 1 and 2nd phosphate groups releasing a pyrophosphate (2 phosphate groups, which are recycled.

§  DNA polymerase III can't polymerize a DNA strand unless a DNA or RNA strand is already attached to the template.

§  An enzyme called DNA primase is needed if the template is bare. DNA primase makes a complimentary primer that is actually a short segment of RNA, usually about 10-12 nucleotides long. At a later stage in replication, the RNA primer is removed and replaced with DNA by DNA Polymerase I.

§  DNA polymerase can only synthesize new DNA in the 5' to 3' direction (of the new strand).

§  Once the fragments have been created, there will be a missing covalent bond (a phosphodiester bond) between the last nucleotide and the replaced primer segment of each Okazaki fragment on the lagging strand. This bond is reformed by an enzyme known as DNA ligase.

Proteins Needed for DNA Replication

Step 3: Proofreading and Repair of newly formed DNA strands

·  DNA polymerase II, IV and V are constantly checking the newly synthesized strand. If they detect a mismatched pair, they will backtrack, cut it out and replace it with the correct pair. They will then proceed in the usual direction to complete the DNA synthesis.

·  There are many other proofreading enzymes known as exonucleases that correct and repair mistakes in the newly forming DNA strands.

·  If the repairs are done immediately to avoid being copied in the next replication. Mistakes that make it through can result in mutations.

Mutations

·  Mutations are errors in the DNA sequence that are inherited.

·  Errors may have a negative impact, a positive impact or no impact detected.

·  A mutation could cause a disease, as it does in cystic fibrosis or it could be good for the evolution of a species, as it was in the increasing size and complexity of the human brain.

More about mutations after we look more closely at protein synthesis.

Awesome Tutorial on DNA Replication!!!!

http://www.wiley.com/college/pratt/0471393878/instructor/animations/dna_replication/index.html