Chapter
9 - DNA
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I. How Did Scientists Discover that Genes are Made of DNA?
A. At the start of modern biology it was not a known fact that genetic information was carried on DNA, just that it was transferred in discrete units called genes.
B. Gregor Mendel (who we will talk about later in a lot of detail) had elucidated the basic rules that governed the transmittal of information from one generation to the next, but had not determined how that transmission was accomplished.
C. A good number of scientists thought that genetic information must be conveyed by proteins, as they are a much more complex molecule than the other possible candidates of nucleic acid or lipids.
D. The solution to the problem came from the works of Fredrick Griffith (1920s) and the group of Oswald Avery, Colin MacLoed, and Maclyn McCarty (1940s).
1. The work was based on the observation that a specific bacterium, Streptococcus pneumonia, produces two distinct forms: a rough-surfaced colony and a smooth-surfaced colony.
a. Rough-surfaced (R) colonies of S. pneumonia were known to be harmless to mice when injected into them.
b. Smooth-surfaced (S) colonies of S. pneumonia were known to be lethal to mice when injected into them.
2. Griffith’s work involved using working with these two strains; he experimented with four groups of mice.
a. Group 1: injected with living R strain bacteria: mice lived.
b. Group 2: injected with living S strain bacteria: mice died.
c. Group 3: injected with killed S strain bacteria: mice lived.
d. Group 4: injected with killed S strain and live R strain: mice died, and live S strain recovered.
e. Griffith concludes that some factor has transferred the ability to become smooth from the dead S strain to the live R strain.
3. Avery and his group take the work up in the 1940s by trying to determine the chemical nature of the factor transmitting the ability to make a colony smooth. After purifying killed smooth cell extract they treat it in various ways and mix it with live R strain before injecting it into mice. (THIS IS COVERED IN MORE DETAIL THAN IN YOUR BOOK - YOU ARE RESPONSIBLE FOR THIS MATERIAL)
a. Group 1: extract treated with lipase (removes lipids): mice die.
b. Group 2: extract treated with protease (removes proteins): mice die.
c. Group 3: extract treated with nuclease (removes nucleic acids): mice live.
d. Group 4: extract not treated (control); mice die.
e. Conclude that the element transferring genetic information has to be nucleic acids.
II. What is the structure of DNA?
A. DNA is structured into long threads called chromosomes.
1. In Porkaryotes the chromosome tends to be a long single circle.
2. In Eukaryotes the chromosome tends to be a number of individual linear pieces.
B. DNA is composed of four nucleotides.
1. DNA is a polymer composed of repeating subunits called monomers, these monomers are the nucleotides.
2. The nucleotides share a common structure.
a. Phosphate group
b. Sugar core, either ribose (RNA) or deoxyribose (DNA)
c. nuclear base.
3. There are four possible nucleotides in DNA, varied in the nuclear base attached.
a. Thymine (T)
b. Cytosine (C)
c. Adenine (A)
d. Guanine (G)
C. DNA is a double helix of two nucleotide strands.
1. The structure of DNA was one of the great “eureka” moments in modern biology, and as such many people worked on it.
2. One of the most influential groups were the team of Wilkins and Franklin, who did much of the structural analysis of DNA.
a. Rosalind Franklin did most of the work that allowed the elucidation of the DNA structure, but she died prior to the Nobel Prize being awarded, and as it can not be awarded to a dead person, her mentor (Wilkins) received the credit.
b. The fateful decision was that the team shared their data with another group, Watson and Crick.
3. Francis Crick and James Watson took the available data and synthesized the double helix model of DNA structure.
a. Nucleotides are bound into long chains with an alternating sugar/phosphate backbone.
b. The bases stick out from the chains.
c. Two chains that are running in opposite directions interact on the level of the bases.
d. Interactions between the bases are due to hydrogen bonds and are specific.
i. A always pairs with T
ii. G always pairs with C
e. The paired strands twist into the familiar double helix, imagine a ladder and twisting the ends in opposite directions.
D. Common written conventions for DNA notation.
a. DNA has a direction, based on the chemical structure of the backbone. While beyond the scope of this course it is important to note that convention is that DNA is written 5’ to 3’ (see below)
b. If one strand is given you can deduce the complementary sequence (the sequence of the other strand) by base pairing rules.
c. The complementary sequence runs in the opposite direction of the first strand (3’ to 5’)
5’- A T G C G C C G T T A G A – 3’ First Strand
3’- T A C G C G G C A A T C T – 5’ Complementary Sequence
E. Even though there are only four possibilities for any one position in a DNA sequence the number of possible sequence variations in a strand of DNA is limitless, allowing immense data storage (think how much data your computer stores and everything is governed by two characters there).
III. How Does DNA Replication Ensure Genetic Constancy During Division?
A. Given the structure of DNA is it possible to see how the molecule could be replicated, considering every piece of information on one strand is duplicated on the opposite strand (in complementary sequence).
B. When DNA is replicated the two new DNA molecules are composed of one old strand and one new strand each, a process called semiconservative replication.
C. DNA is replicated by an enzyme called DNA Polymerase.
1. The Helix is opened by an enzyme called Helicase and the two strands are separated.
2. One strand is replicated in a continuous fashion (Leading Strand) due to the fact that the opening of the helix is proceeding in the same direction as the enzyme can make DNA.
3. One strand is replicated in short discontinuous sections called Okazaki Fragments (Lagging Strand) that result from the DNA Polymerase enzyme having to wait for more of the strand to be uncovered before it can replicated in the opposite direction.
D. DNA Polymerase has the ability to determine if a base it has put in the strand is correct, a property called proofreading, and replace any mismatched bases.
E. While good at its job, proofreading is not perfect and occasionally a wrong base is incorporated into the sequence.