1. Chapter 2 & 3: DNA Structure and Replication
Ms. Gaynor Honors Genetics

2. DNA and Its Structure (Part 2)
From 1953

3. Recall… DNA and RNA are nucleic acids
An important macromolecule in organisms that stores and carries genetic information

4. 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

5. 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

6. DNA has a overall negative charge b/c of the PO4-3 (phosphate group)
A Polynucleotide
MANY nucleotides (“links”) bonded together
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 in Cells 2 broad categories of cells
1. Eukaryotic cells: have nucleus with DNA
DNA is contained in structure called a chromosome
Chromosomes are a LINEAR (line) shape with ENDS called telomeres (protective “caps”)
2. Prokaryotic cells: no nucleus (nucleoid region instead) which contains DNA
DNA is a CIRCULAR shaped chromosome without ENDS (no telomeres)

12. 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

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

14. DNA Double Helix LET’S PRACTICE…
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’

15. DNA Replication (Part 3A-initiation)

16. 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

17. Models of DNA Replication

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

19. Meselson & Stahl Experiment **DNA is semiconservative

20. DNA Replication: a closer look

21. 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.

22. 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.

23. 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

24. 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

25. 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

26. 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!!!

28. 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 (1) RNA primer made by Primase
This new leading strand is made CONTINOUSLY

29. 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

30. 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

32. DNA Replication: Elongation

33. DNA Replication (Part 3C-termination)

34. 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.

35. 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”

36. 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

37. 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

39. DNA Repair