1. Chapter 14: DNA

2. I) Genetic Material – What properties should it have?
Must be a stable molecule that is not easily damaged or altered
DNA has many hydrogen bonds that hold it together
Individually weak but collectively very stable
Contains strong bonds in the “sugar-phosphate backbone”
Phosphodiester Bonds – bond between deoxyribose and phosphate
Double helix structure is energetically stable
Bases on the interior
Negative phosphates on the outside away from each other
DNA damage/errors can be repaired by enzymes in eukaryotes
Telomeres provide added stability to chromosomes
Must be easily and accurately reproduced
Easily reproduced
Enzymes that “unzip” the double helix break hydrogen bonds between bases
Accurately copied
Enzymes use the original template DNA to produce two new strands of DNA
Base sequences serves as the template for new DNA sequences
Proofreading enzymes ensure accurate replication
Hi fidelity – very accurate to conserve genetic code of a species

3. I) Genetic Material – What properties should it have?
Complex for variability
Base sequence determines the sequence of amino acids
Four nitrogenous bases A,T,C,G form 3-base codons
64 possible 3-base codons that code for emaino
Infinite base sequence combinations result in protein variety
Many sequences of codons can code for different proteins
Different sizes of polypeptides from different gene sequences
Parts of one gene may be used for other genes sequences
Eukaryotic Genes:
Introns – do not code for polypeptides
May code for regulatory RNA or nothing
Introns are highly variable and are used for paternity and forensics
Exons – sequences that code for polypeptides

4. II) Experiments that Proved DNA is the Hereditary Material of Organisms
Frederick Griffith (1928)
Bacterial Transformation – a “transforming principle” changed the non-virulent bacteria (Streptococcus pneumonia ) into virulent (deadly) bacteria
Genetic Material was resistant to heat treatment – could not protein based because proteins denature in high temperatures
Griffith's experiments proved that the genetic make-up of the non-pathogenic strain was altered by one of the components of the heat-killed pneumonia-causing bacterium, causing the rough cell to become pathogenic
Avery-McCarty-MacLeod (1944)
Used heat to kill the virulent Streptococcus pneumonia bacteria and eliminated RNA, DNA, carbohydrates, lipids and proteins
Each molecule was added to a culture of live non-virulent bacteria to determine which was responsible for changing them into virulent bacteria.
DNA was the only molecule that transformed the non-virulent cells into virulent cells
They concluded DNA was in fact the genetic material within cells that transformed the bacteria in Griffith’s experiment.

6. Francis Crick and James Watson (1953)
Hershey and Chase (1952)
Determined the genetic material was the molecule DNA
Traced the movement of DNA from viruses into bacterial cells
Proved DNA was the molecule being transferred NOT protein
Rosalind Franklin (1952)
Studied DNA using X-Ray crystallography
Determined the double helix structure (two strands, NOT 3)
Determined the structure of the sugar phosphate backbone
Could not interpret the base pairing
Erwin Chargaff (1952)
Determined the ratio of DNA bases to be equal
A = T C = G
Ratios are also species specific
Francis Crick and James Watson (1953)
Used modeling to elucidate the final structure of DNA
Determined the base pairing of DNA from Chargaff’s work
Determine the correct structure using Franklin’s data
Proposed how DNA could replicate by “unzipping”
Could not have done their work without Franklin’s results

7. Hershey and Chase Experiment

8. Rosalind Franklin’s X-Ray Diffraction

9. Chargaff’s Rule
Humans: 60% A-T 40% C-G Wheat: 55% A-T 45% C-G

10. James Watson and Friends

11. You would think I am meeting Billy Joel!
Watson and Bolen
You would think I am meeting Billy Joel!

12. Messelson and Stahl (1958) Determined how DNA replicates
Modeled semiconservative replication
The old or template strand is copied and becomes part of the new DNA molecule

13. III) DNA Structure
DNA, and in some cases RNA, is the primary source of heritable information.
1. Double Helix
Two alpha helices of deoxyribonucleic acid
Contains repeating subunits called nucleotides
Phosphate, sugar, nitrogenous base
2. Bonding
Hydrogen bonds BETWEEN the nitrogenous bases
Many weak bonds results in collectively strong bonding
Phosphodiester Bonds
Strong bonds in sugar-phosphate backbone
3. Complementary (opposite) Base-Pairing
Adenine and Thymine pair
Cytosine and Guanine pair
Result of specific hydrogen bonding between bases
Purines: Adenine and Guanine
Pyrimidine's: Cytosine, Uracil, Thymine (PYRamid stones were CUT)
One side of the double helix complements the other side

16. 4. Antiparallel Helices
Each side of the DNA molecule is oriented in the opposite directions
Permits base pairing
Important in understating direction of replication and location of enzymes and other proteins
Based upon the numbering of
the carbons in the deoxyribose
molecule

17. 5. Semiconservative Replication
Each DNA molecule is copied from the original strand
Two copies of DNA produced in replication
Each strand contains half new and half template DNA

18. IV) DNA Replication
Genetic information is transmitted from one generation to the next through DNA or RNA
Non-eukaryotic organisms have circular chromosomes
One replication origin – point where DNA replication begins
Eukaryotic organisms have multiple linear chromosomes
Multiple replication origins – results in efficient replication rates – it saves time
Exceptions to this rule:
Plasmids - small extra-chromosomal, double-stranded circular DNA molecules
Prokaryotes, viruses and eukaryotes can contain plasmids
Replicate plasmids at the same time as the main circular chromosome

19. Eukaryotic Chromosome Structure
- Large cluster of histone proteins
Proteins that regulate gene expression
Bind to specific DNA sequences

20. New DNA molecules are synthesized from a template or original DNA strand
Topoisomerase – relaxes the supercoiling of DNA
Gyrase – relieves strain on the helix as it is uncoiled – flatten the DNA
DNA Helicase – breaks hydrogen bonds between nitrogenous bases
“Unzip DNA”
DNA Primase – forms a primer of RNA in the 3’5’
Starting point for DNA polymerase to attach and begin copying
DNA polymerase can only add to an existing double strand
DNA Polymerase – synthesizes new DNA from template
“Reads” and moves along the DNA template in the 3’  5’ direction
Adds nucleotides to the 3’ ends of the DNA template
Exonucleases – remove incorrect DNA bases
DNA polymerase I can move backwards one base to remove errors
Ligase – links Okazaki fragments on the lagging strand
Lagging strand – new DNA produced in short segments
Leading strand – new DNA produced in one continuous strand

21. Bi-Directional Replication in DNA 1 Bi-Directional Replication in DNA 2 Replication 3 Replication 4

22. IV) Special Cases of DNA Replication
Retroviruses
Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA  DNA
Reverse transcriptase - enzyme that copies the viral RNA genome into DNA.
This DNA integrates into the host genome
Viral genes become transcribed and translated for the assembly of new viral progeny.
Examples of retroviruses: HIV,

23. DNA in Prokaryotes vs Eukaryotes
Circular Chromosome
Located in Cytoplasm
No histones or supercoiling
No introns
All DNA codes for protein
Linear Chromosomes
Multiple chromosomes
Located in Nucleus
Histones and supercoiling of DNA
Contains introns and Exons
Introns – non-coding DNA sequences – do not code for protein
Exons – DNA base sequences that code for functional protein

24. TEST TOPICS 1 Long Free-Response, 2 short response (20 points)
DNA structure and how it contributes to stability
Bonds
Base-pairing
DNA replication
Use of template, bi-directional replication
DNA structure in eukaryotes & prokaryotes
DNA replication in eukaryotes & prokaryotes
Know the contributions of the following:
Griffith – transforming principle was not protein
Avery, MacLeod, McCarty – genetic material is DNA
Hershey & Chase – DNA in bacteriophages (viruses) is transferred to bacteria
Rosalind Franklin – DNA is a helix
Charfgaff – ratio of A=T and C=G
Watson and Crick – Chargaff's ratios suggest base pairing
Double helix has bases on inside, phosphate-sugar backbone on outside