1. Structure & Replication of DNA & RNA
2.6, 2.7, & 7.1

2. Essential Idea: Structure of DNA allows efficient storage of genetic information.
2.6
Structure of DNA
Understandings:
The nucleic acids DNA and RNA are polymers of nucleotides
DNA differs from RNA in the number of strands present, the base composition and the type of pentose
DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs
Application:
Crick and Watson elucidation of the structure of DNA using model making
Skill:
Draw simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases

3. Essential Idea: Genetic information in DNA can be accurately copied and can be translated to make the proteins needed by the cell.
2.7
DNA replication, transcription and translation
Understandings:
The replication of DNA is semi-conservative and depends on complementary base pairing
Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds
DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template
Applications:
Use Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain reaction (PCR)
Skills:
Analyze Meselson &Stahl’s results to obtain support for the theory of semi-conservative replication of DNA

4. Essential Idea: The structure of DNA is ideally suited to its function.
7.1
DNA Structure and Replication
Understandings:
Nucleosomes help to supercoil the DNA
DNA structure suggested a mechanism for DNA replication
DNA polymerases can only add nucleotides to the 3’ end of a primer
DNA replication is continuous on the leading strand and discontinuous on the lagging strand
DNA replication is carried out by a complex system of enzymes
Some regions of DNA do not code for proteins but have other important functions
Applications:
Rosalind Franklin’s and Maurice Wilkins’ investigation of DNA structure by x-ray diffraction
Use of nucleotides containing dideoxyribonucleic acid to stop DNA replication in preparation of samples for base sequencing
Tandem repeats are used in DNA profiling
Skills:
Analyze results of the Hershey and Chase experiment providing evidence that DNA is the genetic material
Utilize molecular visualization software to analyze the association between protein and DNA within a nucleosome

5. I. Nucleotides Nitrogenous Bases:
-Purines – Adenine (A) and Guanine (G)
-Pyrimidines – Cytosine (C), Thymine (T), Uracil (U)

6. Polymer of nucleotides
II. DNA vs. RNA
DNA
RNA
Polymer of nucleotides
Deoxyribose sugar
Ribose sugar
Double stranded
Single stranded
Bases = A, T, G, C
Bases = A, U, G, C
DNA is a more stable form that stores the genetic blueprint for cells.
RNA is a more versatile form that transfers the genetic information for decoding.

8. III. DNA Structure

9. III. DNA Structure -Strands are antiparallel
-Complimentary Base Pairing
Phosphodiester bonds between nucleotides on backbone

11. IV. Nature of Science
A. Hershey and Chase – 1952 – determined DNA was the genetic material by separately radiating the protein and DNA portions of a bacteriophage – found that virus inserted DNA into bacteria cells, not protein

12. Discuss as a table
Explain Hershey and Chase’s experiment and results to each other.

13. B. Chargaff’s Rule – amount of A in an organism’s DNA is equal to the amount of T, and G is equal to C

14. C. Rosalind Franklin and Maurice Wilkins – X-ray diffraction of DNA indicated helical pattern, positions of bases and sugars, distance between bases, and tightness of coiling

15. 1. Used models – pioneered by Linus Pauling
Watson & Crick – 1953
1. Used models – pioneered by Linus Pauling
2. Stole pictures from Franklin
3. Structure also indicated a mechanism for replication because of the complimentary base pairing
Using trial and error they built several models.
First was triple helix
Bases on outside, sugar and phosphate on the inside.
Nitrogenous bases were not initially configured correctly and did not demonstrate complementarity.

16. E. Meselson & Stahl - Made parent strand with “heavy” N, added free floating DNA nucleotides with “light” N
1st generation – new strands were 50% light, 50% heavy
2nd generation – half of the strands were 50/50, other half were all light

18. Discuss as a table
Explain Meselson & Stahl’s experiment and results to each other.

19. Relieves strain of unwound DNA SSBs
V. Replication Enzymes
Enzyme
Function
Helicase
Unzips & unwinds DNA
Gyrase
Relieves strain of unwound DNA
SSBs
Help hold DNA open and stabilize it
Primase
Builds RNA Primer
DNA Polymerase III
Builds new DNA strand
DNA Polymerase I
Replaces RNA primer with DNA
DNA Ligase
Joins Okazaki fragments together

20. VI. The Process A. The Steps
Helicase unzips DNA (breaks hydrogen bonds) creating a replication bubble at the origin of replication
Multiple origins per chromosome in eukaryotes
Each side of bubble has replication fork
Bubble enlarges as replication proceeds until bubbles meet

21. 2. Primase builds a short primer of RNA nucleotides (5 – 10 bases)

22. DNA Polymerase III builds the complimentary strand of DNA in the 5’  3’ direction
a. Free-floating DNA nucleotides move in to match up with parent strand, DNA polymerase III moves along and binds them together with phosphodiester bonds

23. 4. DNA Polymerase I replaces RNA primer with DNA nucleotides

24. B. Leading and Lagging Strands
New nucleotides must be added on to the 3’ end
Leading strand – Bases easily added as DNA is unzipped

25. Lagging Strand – has a delay
a. Section unzips, then strand is built back towards origin
b. Results in chunks called Okazaki fragments
c. DNA ligase bonds Okazaki fragments together after primer is replaced

26. VII. Speed and Accuracy
~4000 nucleotides per second
Few errors, but also have proof-reading mechanisms Enzymes (exonucleases) cut out mistake and replace with correct base (also activated by mutations such as by uv radiation, x-rays, etc.)

27. VIII. DNA Packaging
B. Nucleosomes – 2 each of 4 types of histone (8 total) with DNA wrapped around it twice
Histones – proteins that associate with DNA to help it coil
1. DNA is
negatively
charged,
histones are
positively
charged
Linker DNA – Between nucleosomes, associated with 5th type of histone
Helps with supercoiling for cell division
Controls gene expression – tightly coiled regions cannot be expressed

28. IX. Non-Coding DNA
Coding sequences code for proteins = GENES (only about 1.5% of DNA in humans)
Non-coding regions
1. Produce tRNA & rRNA
2. Regulate gene expression – can act as enhancers or silencers

29. Repetitive Sequences (moderately or highly)
% of genome (over 50% in eukaryotes)
2. Telomeres (ends of chromosomes) – protect coding regions - during replication, enzymes can’t get all the way to the end of the chromosome  lose a bit of DNA each time

30. X. DNA Sequencing
A. DNA sequencing refers to the process by which the base order of a nucleotide sequence is elucidated.
1. The most widely used for DNA sequencing involves the use of chain- terminating dideoxynucleotides.
2. Dideoxynucleotides (ddNTPs) lack the 3’-hydroxyl group necessary for forming a phosphodiester bond.
3. ddNTPs prevent further elongation of a nucleotide chain and effectively terminate replication.
4. The resulting length of a DNA sequence will reflect the specific nucleotide position at which the ddNTP was incorporated.