1. DNA Strcuture and Replication (PART 2)
Ms. Gaynor AP Biology

2. DNA and Its Structure
From 1953

3. What is the Double Helix?
Shape of DNA
Looks like a twisted ladder
2 coils are twisted around each other
Double means 2
Helix means coil

4. The Structure of DNA Made out of nucleotides
Includes a phosphate group, nitrogenous base and 5-carbon pentose sugar
Nucleotide Structure
1 “link” in a DNA chain

5. Nucleoside Structure

6. DNA has a overall negative charge b/c of the PO4-3 (phosphate group)
A Polynucleotide
MANY nucleotides (“links”) bonded together
Nucleotide Structure
DNA has a overall negative charge b/c of the PO4-3 (phosphate group)

7. The Structure of DNA Backbone Backbone = alternating P’s and sugar
Held together by COVALENT bonds (strong)
Inside of DNA molecule = nitrogen base pairs
Held together by HYDROGEN bonds (weaker)
Backbone

8. The covalent that holds together the backbone
Phosphodiester Bond
The covalent that holds together the backbone
Found between P & deoxyribose sugar
STRONG!!!

9. Minor Groove
Major Groove

10. DNA is antiparallel
Antiparallel means that the 1st strand runs in a 5’ 3’ direction and the 2nd 3’ 5’ direction
THEY RUN IN OPPOSITE or ANTIPARALLEL DIRECTIONS
P end is 5’ end (think: “fa” sound)
-OH on deoxyribose sugar is 3’ end
5’ and 3’ refers to the carbon # on the pentose sugar that P or OH is attached to

11. DNA Bonding Purines (small word, big base) Pyrimidines
Adenine
Guanine
Pyrimidines
(big word, small base)
Cytosine
Thymine
Chargaff’s rules
A=T, C=G
Hydrogen Bonds attractions between the stacked pairs; WEAK bonds

12. Why Does a Purine Always Bind with A Pyrimidine?

13. DNA Double Helix LET’S PRACTICE… Watson & Crick said that…
Watson & Crick said that…
strands are complementary; nucleotides line up on template according to base pair rules (Chargaff’s rules)
A to T and C to G
LET’S PRACTICE…
Template: ’AATCGCTATAC3’
Complementary strand: 3’
TTAGCGATATG5’

14. REVIEW…
______ discovered the double helix structure of DNA and won a Nobel prize for this work in 1962
______ made photo 51, which helped discover the correct helical shape of DNA
______ worked with pneumococcus bacteria and mice to conclude an inheritance molecule is present in cells
______ worked with fruit flies and discovered genes are linked (connected to) chromosomes (chunks of DNA)
______ worked with bacteriophages and discovered that DNA not protein is the inheritance molecule in cells
______ worked with pneumococcus bacteria and test tubes to discover DNA not RNA or protein is a transforming agent
______ worked with x-ray crystallography and created pictures of DNA; won a Nobel prize in 1962 for this work
______ discovered DNA in any species contains equal amounts of adenine and thymine and equal amounts of guanine and cytosine; credited with forming the “base pair rules”
______ worked with garden pea plants and was the first scientist to study inheritance patterns

15. Label the DNA strands shown below. Label a deoxyribose sugar molecules
a phosphate molecules (PO43-)
Hydrogen bonds
Label the phosphodiester bonds
The 5’ and 3’ ends
Label the bases that are not already labeled
Purines
Pyrimidines
5. (3’ end)
5. (5’ end)
3. (2 bonds)
6. T 1. 2.
6. A
3. (3 bonds)
6. C 4.
6. G
A and G
C and T
5. (5’ end)
5. (3’ end)

16. A nucleotide is made of three parts: a ________ group, a five carbon __________________, and a nitrogen containing _____________________. Nucleotides are monomers for _______ and ________.
In a single strand of DNA, the phosphate group binds to the _______ of the next group to form the _____________ of the molecule. What bond holds together the sugars and phosphates in DNA? _______________
The _______ _______ form the middle of the DNA molecule (rungs or steps of the ladder) and are held together by _________________ bonds.
Purines have _____ rings of carbon, and pyrimidines have ______ ring.
Purines include ___________ base and ____________ base.
Pyrimidines include __________ base and ____________ base.
In DNA, thymine is complementary to ________________ ; cytosine is complementary to _____________.
Thymine and _____________________ are _____ hydrogen bonds together.
Cytosine and _____________________ are _____ hydrogen bonds together.

17. DNA Replication (initiation)

18. DNA Replication DNA Replication = DNA  DNA
Parent DNA makes 2 exact copies of DNA
Why??
Occurs in Cell Cycle before MITOSIS so each new cell can have its own FULL copy of DNA

19. Models of DNA Replication

20. DNA Replication How does it occur?
Matthew Meselson & Frank Stahl
Discovered replication is semiconservative
PROCEDURE  varying densities of radioactive nitrogen (Nitrogen is in DNA)

21. Meselson & Stahl Experiment **DNA is semiconservative

22. DNA Replication: a closer look

23. DNA Replication Steps:
Initiation
involves assembly of replication fork (bubble) at origin of replication
sequence of DNA found at a specific site
Elongation
Parental strands unwind and daughter strands are synthesized.
the addition of bases by proteins
Termination:
the duplicated chromosomes separate from each other. Now, there are 2 IDENTICAL copies of DNA.

24. BEGINNING OF DNA REPLICATION
Segments of single-stranded DNA are called template strands.
Copied strand is called the complement strand (think “c” for copy)
BEGINNING OF DNA REPLICATION
(INITIATION)
Gyrase (type of topoisomerase)
relaxes the supercoiled DNA.
DNA helicase (think “helix”)
binds to the DNA at the replication fork
untwist (“unzips”) DNA using energy from ATP
Breaks hydrogen bonds between base pairs
Single-stranded DNA-binding proteins (SSBP)
stabilize the single-stranded template DNA during the process so they don’t bond back together.

25. Supercoiled DNA relaxed by gyrase & unwound by
base pairs 5’ 3’
Supercoiled DNA relaxed by gyrase & unwound by
helicase
SSB Proteins
Helicase
ATP
Gyrase
SSB Proteins

26. DNA Replication (elongation)

27. DNA Replication (Elongation)
After SSBP’s bind to each template…
RNA Primase binds to helicase
primase is required for DNA synthesis
Like a “key” for a car ignition
makes a short RNA primers
Short pieces of RNA needed for DNA synthesis
DNA polymerase
adds nucleotides to RNA primer  makes POLYNUCLEOTIDES (1st function)
After all nucleotides are added to compliment strand…
RNA primer is removed and replaced with DNA by DNA polymerase (2nd function)
DNA ligase
“seals” the gaps in DNA
Connects DNA pieces by making phosphodiester bonds

28. Supercoiled DNA relaxed by gyrase & unwound by
base pairs 5’ 3’
Supercoiled DNA relaxed by gyrase & unwound by
helicase + proteins:
SSB Proteins
Helicase
ATP
DNA Polymerase 1 2
Gyrase
RNA primer replaced by DNA Polymerase & gap is sealed by ligase
RNA Primer
primase
DNA Polymerase
Leading strand

29. Elongation 5’  3’ direction only!!! Antiparallel nature:
Sugar (3’end)/phosphate (5’ end) backbone runs in opposite directions
one strand runs 5’  3’,
other runs 3’  5’
DNA polymerase only adds nucleotides at the free 3’ end of NEW STRAND forming new DNA strands in the
5’  3’ direction only!!!

31. Elongation (con’t) Leading (daughter) strand
NEW strand made toward the replication fork (only in 5’  3’ direction from the 3’  5’ master strand
Needs ONE RNA primer made by Primase
This new leading strand is made CONTINOUSLY

32. Elongation (con’t) Lagging (daughter) strand
NEW strand synthesis away from replication fork
Replicate DISCONTINUOUSLY
Creates Okazaki fragments
Short pieces of DNA
Okazaki fragments joined by DNA ligase
“Stitches” fragments together
Needs MANY RNA primer made by Primase

33. Supercoiled DNA relaxed by gyrase & unwound by
base pairs 5’ 3’
Supercoiled DNA relaxed by gyrase & unwound by
helicase + proteins:
SSB Proteins
DNA Polymerase
Lagging strand
Okazaki
Fragments 1
Helicase
ATP 2 3
Gyrase
RNA primer replaced by
DNA Polymerase & gap is
sealed by DNA ligase
RNA Primer
primase
DNA Polymerase
5’  3’
Leading strand

35. DNA Replication: Elongation

36. DNA Replication (termination)

37. Telomeres
Euchromatin = coding region of DNA; contains active genes (in both prokaryotes & eukaryotes)
Not all euchromatin is necessarily transcribed
THINK: “Eu” need Euchromatin
Heterochromatin = noncoding region of DNA; contains active genes (only in eukaryotes)
Thought to protect the genes while they are not in use/ “turned on” in transcription

38. Termination (Telomeres)
Short repeats of “G” base found at END of LINEAR chromosomes in eukaryotes
protect ends of linear chromosomes
The repeated sequence of GGGTTA make up the human telomeres.
Telomerase is the enzyme that makes telomeres.

40. Telomeres, Aging & Cancer
Telomeres get shorter as cell divides leads to aging???
Most cancers come from body cells.
Cancers cell have ability to divide indefinitely.
Normal cells limited to ~50-75 divisions  stop making telomerase.
85–90% cancer cells continue to make high levels of telomerase & are able to prevent further shortening of their telomeres.
Leads to “immortality”

41. Mistakes Made during DNA Replication
Mutation
Change in DNA (genetic material)
Frameshift(s)
extra or missing base(s).
Substitutions
when the wrong nucleotide is incorporated (mismatch mutation).
Deletions
Nucleotides are deleted shortening the DNA

42. DNA Repair Errors occur 1/10 billion nucleotides Mismatch repair
(Humans have 3 billion base pairs in their DNA)
Mismatch repair
DNA polymerase (yes…it’s 3rd function)
“Proofread” new DNA
Like the “delete” key on computer
Excision (“cut out”) repair
Nuclease

44. DNA Repair