2. Chromosomal Landscapes
Refer to Figure 1-7 from Introduction to Genetic Analysis, Griffiths et al., 2012.

3. Human Chromosomal Landscapes
Refer to Figure 1-8 from Introduction to Genetic Analysis, Griffiths et al., 2012.

4. Relationship between Genotype and Phenotype
Molecular Basis for
Relationship between Genotype and Phenotype
genotype
DNA
DNA sequence
transcription
replication
RNA
translation
amino acid
sequence
protein
function
phenotype
organism

5. DNA replication is discontinuous.
Replication of DNA is
semiconservative.
Each strand serves
as a template.
The two strands
separate from each
other when
hydrogen bonds
are broken.
Replication of DNA is
semiconservative.
Each strand serves
as a template.
The two strands
separate from each
other when
hydrogen bonds
are broken.
New strands are synthesized by the addition of nucleotides with bases complementary to those of the template.
DNA replication is discontinuous.
Two identical double helices result.
New strands are synthesized by the addition of nucleotides with bases complementary to those of the template.
DNA replication is discontinuous.
Two identical double helices result.
Refer to Figure 7-11 from Introduction to Genetic Analysis, Griffiths et al., 2012.

6. DNA polymerization requires DNA polymerase.
Refer to Figure 7-15 from Introduction to Genetic Analysis, Griffiths et al., 2012.

7. At least 5 DNA polymerases are known in E. coli .
DNA polymerase I (pol I):
adds nucleotides in 5’ to 3’ direction
removes mismatched bases in 3’ to 5’ direction
degrades double-stranded DNA in 5’ to 3’ direction
DNA polymerase II (pol II):
repairs interstrand cross-links
DNA polymerase III (pol III):
catalyzes DNA synthesis at replication fork in
5’ to 3’ direction and only adds nucleotides at 3’ end of growing strand

8. Overview of DNA Synthesis
DNA polymerases synthesize new strands in 5’ to 3’ direction.
Primase makes RNA primer.
Lagging strand DNA consists of Okazaki fragments.
In E. coli, pol I fills in gaps in the lagging strand and removes RNA primer.
Fragments are joined by DNA ligase.

9. DNA Replication at Growing Fork
DNA polymerases add nucleotides in 5’ to 3’ direction.
Because of antiparallel nature, synthesis of DNA is continuous for one strand and discontinuous for the other strand.

10. DNA Replication:
Synthesis of Lagging Strand
Several components and steps are involved in the discontinuous synthesis of the lagging strand.
Note that DNA polymerases move in 3’ to 5’ direction on the template DNA sequence.

11. DNA Replication:
Synthesis of Lagging Strand
DNA extended from primers are called Okazaki fragments.
In E. coli, pol I removes RNA primers and fills in the gaps left in lagging strands.
DNA ligase joins these pieces.

12. Replisome and Accessory Proteins
Looping of template DNA for the lagging strand allows the two new strands to be synthesized by one dimer.
pol III holoenzyme is a complex of many different proteins.
Refer to Figure 7-20 from Introduction to Genetic Analysis, Griffiths et al., 2012.

13. DNA polymerases can extend (but cannot start) a chain.
Priming DNA Synthesis
DNA polymerases can extend (but cannot start) a chain.
Primase enzyme makes short RNA primer sequence complementary to template DNA.
DNA polymerase extends RNA primer with DNA.
Primosome is a set of proteins that are involved in the synthesis of RNA primers.
Refer to Figure 7-20 from Introduction to Genetic Analysis, Griffiths et al., 2012.

14. Supercoiling results from separation of template strands during DNA replication.

15. Helicases and Topoisomerases
Helicase enzymes disrupt hydrogen bonding between complementary bases.
Single-stranded binding protein stabilizes unwound DNA.
Unwound condition increases twisting and coiling, which can be relaxed by topoisomerases (such as DNA gyrase).
Topoisomerases can either create or relax supercoiling.
They can also induce or remove knots.

16. Nucleosome assembly follows thereafter.
Chromatin assembly factor I (CAF-I) and histones are delivered to the replication fork.
CAF-I and histones bind to proliferating cell nuclear antigen (PCNA), the eukaryotic version of clamp protein.
Nucleosome assembly follows thereafter.
Refer to Figure 7-23 from Introduction to Genetic Analysis, Griffiths et al., 2012.

17. Overview of DNA Synthesis
DNA polymerases synthesize new strands in 5’ to 3’ direction.
Primase makes RNA primer.
Lagging strand DNA consists of Okazaki fragments.
In E. coli, pol I fills in gaps in the lagging strand and removes RNA primer.
Fragments are joined by DNA ligase.