1. The flow of Genetic information

2. DNA Replication DNA is a double-helical molecule
Watson and Crick Predicted Semi-conservative Replication of DNA
The mechanism: Strand separation, followed by copying of each strand.
Each separated strand acts as a template for the synthesis of a new complementary strand.
Each strand of the helix must be copied in complementary fashion by DNA polymerase
DNA replication takes place in a semiconservative manner. That is, a parent double helix forms two daughter double helices, each composed of one parent DNA stand and on newly synthesized stand.

3. Semiconservative DNA Replication
Two identical new copies of the DNA double helix are produced during replication
Each new strand is complementary to its old template strand
In each new helix, one strand is the old template and the other is newly synthesized.

4. Semiconservative DNA Replication

5. Bacteria have circular chromosome with single origin of replication.
E. coli genome size = 4.6 X 106 bp
Bacteria have circular chromosome with single origin of replication.
Replication rate is ~1000 base pairs per second.
Duplicate chromosome in 38 minutes.
Eukaryotes have larger genomes 3 X 109 bps
Rate of Eukaryote chromosome replication is slower
But because eukaryote chromosomes have multiple origins of replication, it takes about the same amount of time to replicate complete genome.
Eukaryote
prokaryote

6. DNA Replication

7. Stages of DNA Replication
Initiation: perpriming complex
Elongation: RNA primer and DNA polymerase
Termination
Initiation
DNA should unfold before the beginning of replication. This process is performed by a group of proteins called the prepriming complex:
The first important protein is a small enzyme called DNAa protein.
20-50 monomers of this enzyme will recognize and bind to a consensus sequence called the origin of replication (a region on DNA rich in the nucleotides Adenosine ad Thymidine).
DNAa then causes a local opening or local melting to appear.
This process is energy consuming; the energy is obtained by DNAa form of ATP.

9. Initiation
Once the strands are separated, a protein called single strand binding protein (SSB protein) will bind to each strand preventing their refolding into a double helical form.
The binding of SSB proteins does not require energy.
Another function of SSB proteins is to protect the single DNA strands from the action of endonucleases. Since the single DNA strand is a substrate for these enzymes.
Helicase
Is an enzyme that uses energy (ATP) to separate the two DNA strands apart beginning at the local opening formed by DNAa protein. Its action is focused at the replication fork.

11. Endonucleases and Exonucleases

12. Priming and Replication
DNA polymerase III is unable to form a nucleotides sequences from scratch it requires a primer or an already existing nucleotide which is RNA primer
The starting point for DNA polymerase is a short segment of RNA known as an RNA primer.
The primer is RNA strand complementary to the DNA template synthesized by an enzyme known as RNA polymerase or Primase.
The RNA primer consists of about 10 ribonucleotides complementary to the sequence on the DNA strand.
The DNA polymerase (once it has reached its starting point as indicated by the primer) then adds nucleotides one by one in an exactly complementary manner, A to T and G to C.

14. Elongation and replication
Primase Complex Synthesizes short RNA primers.
The class of enzymes which perform DNA synthesis are called the polymerase enzymes. The polymerases can only read DNA in a 3` →5` direction  they synthesize DNA only in 5` to 3` direction.
The DNA double helix has the following polarity:
Leading strand 3` → 5` lagging strand is 5` → 3`
DNA polymerase uses the parent strands as template and synthesizes a new 5` → 3` strand U

15. DNA Replication is Semidiscontinuous
Synthesis along the leading strand is continuous and is carried out by polymerase III. On the other hand, synthesis along the lagging strand is discontinuous and is produced in fragments called Okazaki fragments. and takes place via two enzymes: polymerase III and polymerase I.

16. DNA Replication

17. Replication of lagging strand by Okazaki fragments.
-The enzyme responsible for synthesis of these fragments is polymerase III
- It requires an RNA primer
the synthesis takes place from 5` → 3`, in an opposite direction to that in which the replication fork progresses.
As the replication fork spreads and more of the double helix is unfolded, an RNA primer is added to the lagging strand at the replication fork, the polymerase III then proceeds in adding deoxynudeotides to the OH end of the RNA primer, until it reaches another primer.
A gap or a nick between the Okazaki fragments and the RNA primer.
The nick is recognized by polymerase I, that removes the ribonucleotides of the primer and replace them by deoxynucleotides complementary to the parent DNA strand
This forms a discontinuous strand with stretches of DNA separated by gaps or nicks.
Another enzyme, ligase, seals these nicks by forming phosphodiester bonds. The polymerase I also replaces the RNA primer on the leading strand with deoxynucleotides.

18. Replication of lagging strand by Okazaki fragments.

19. The Enzymology of DNA Replication
If Watson and Crick were right, then there should be an enzyme that makes DNA copies from a DNA template
In 1957, Arthur Kornberg and colleagues demonstrated the existence of a DNA polymerase -
Three DNA polymerases in E. coli
DNA polymerase I – DNA repair and participates in synthesis of lagging strand
DNA polymerase II – DNA repair
DNA polymerase III – major polymerase involved in DNA replication.
Elongation involves DnaB helicase unwinding, SSB binding to keep strands separated.
Primase Complex synthesizes short RNA primers.
DNA polymerase grinding away on both strands
Topoisomerase II (DNA gyrase) relieves supercoiling that remains

20. DNA Polymerase also has proof reading function
The polymerization reactions have an error rate of 1 mistake for every 100,000 base pairs incorporated (1 X 10-5 errors per base)
Polymerases have proof reading functions. As they synthesize DNA, they double check for any incorrectly paired bases.
If any mismatches are found, they are removed and replaced by the correct base This means that polymerase III has 3` → 5` exonuclease activity or it proofreads DNA from 3` → 5`.
Therefore proof reading function helps eliminate errors which could lead to detrimental mutations.
However proof reading exonuclease has error rate of 1 mistake for every 100 base pairs (1 X 10-2 errors per base)
Overall error rate is 1 X 10-7 errors per base.
Polymerase I has a 5` → 3` exonuclease activity in order to remove the RNA primer. In addition to that, it also possesses 3` → 5` exonuclease activity which aims at proofreading the DNA sequence that has replaced the RNA primer.

21. Polymerase action

22. Ligase connects loose ends. Used NAD+ in phosphoryltransfer reaction,
DNA polymerase I has 5’ to 3’ exonuclease activity that removes RNA primer. Also has 5’ to 3’ DNA polymerase activity to fill in the gap. (proofreading 3’-5’ exonuclease activity)
Ligase connects loose ends. Used NAD+ in phosphoryltransfer reaction,
DNA Polymerase I/ Ligase Required to Join
Okazaki Fragments

23. Polymerase I has a 5`→ 3` exonuclease activity in order to remove the RNA primer. In addition to that, it also possesses 3`→ 5` exonuclease activity which aims at proofreading the DNA sequence that has replaced the RNA primer.

24. DNA Replication

25. Enzymes that relief supercoiling (Super-twisting )
During the replication the two strand of the DNA should be away from each other
Supercoiling should be removed  so the DNA have to rotate opposite of the direction of the coiling but this method costs energy and lead to another supercoiling
Topoisomerase enzymes solve this problem. There are two types:
Topoisomerase I works only on one strand of the DNA and cut that strand, then allows the other strand to pass through to solve the supercoil, then it connects the strand again [nuclease activity and ligase activity]
Topoisomerase II works on the two strands of the DNA at the same time, and it is more efficient than topoisomerase I. Topoisomerase II cuts both strands of the DNA, allows the other one to move through it, and basically it will relieve supercoil.

26. Supercoiling During DNA strand separation

27. Enzymes that Relief Supercoiling

28. DNA Replication in Eukaryotes Eukaryotic DNA Polymerases
Occurs similarly to what occurs in prokaryotes.
Multiple origins of replication
Replication is slower than in prokaryotes.
5 different DNA polymerases in Eukaryotes.
Eukaryotic DNA Polymerases
Alpha (Pol  )– Primer synthesis and DNA repair
Beta – DNA repair
Gamma – Mitochondrial DNA replication
Delta (Pol  )– Leading and lagging strand synthesis, and DNA repair
Epsilon (Pol  ) – Repair and gap filling on lagging strand.

29. Termination of Replication
Termination occurs at ter (terminus )region of E. coli chromosome.
ter region rich in Gs and Ts, signals the end of replication.
Terminator utilization substance (Tus) is a protein which binds to ter region.
Tus prevents replication fork from passing by inhibiting helicase activity.

30. The End

31. DNA Repair A fundamental difference from RNA, protein, lipid, etc.
All these others can be replaced, but DNA must be preserved
Cells require a means for repair of missing, altered or incorrect bases, bulges due to insertion or deletion, UV-induced pyrimidine dimers, strand breaks or cross-links
Two principal mechanisms: methods for reversing chemical damage and excision repair.

32. Repair of UV Induced Thymine Dimers

33. General excision-repair pathway
Excision-repair systems scan DNA duplexes for mismatched bases, excise the mispaired region and replace it

34. Repair of damage resulting from the deamination of cytosine
Deamination of cytosine to uracil is one of most common forms of DNA damage
DNA glycosylases cleave bases at N-glycosidic linkages. Leaving sugar-phosphate backbone.
Endonuclease identifies abscent base and sugar phosphate.
Gap then filled in by DNA polymerase and ligase.