Chapter 16: The Molecular Basis of Inheritance -REVIEW

DNA Structure and Replication

Structure of DNA

The structure of DNA is fundamental to its function as the genetic material. DNA is a double helix composed of two antiparallel strands of nucleotides.

• Nucleotide Composition: Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine [A], thymine [T], cytosine [C], or guanine [G]).

• Base Pairing: Adenine pairs with thymine via two hydrogen bonds, and cytosine pairs with guanine via three hydrogen bonds.

• Backbone: The sugar-phosphate backbone is held together by phosphodiester bonds.

• Double Helix: The two strands run in opposite directions (antiparallel), one 5' to 3' and the other 3' to 5'.

• Chargaff's Rules: In any DNA sample, %A = %T and %C = %G. For example, if T = 39%, then A = 39%, and C + G = 22% (C = 11%, G = 11%).

Key Terms:

• Antiparallel: The two DNA strands run in opposite directions, which is essential for replication and function.

• Hydrogen Bonds: Hold the two DNA strands together between complementary bases.

• Phosphodiester Bonds: Link nucleotides within a single DNA strand.

Example: If A = 19%, then T = 19%, and C + G = 62% (C = 31%, G = 31%).

Evidence That DNA is the Genetic Material

• Griffith's Transformation Experiment: Demonstrated that a substance from dead bacteria could genetically transform living bacteria.

• Hershey-Chase Experiment: Showed that DNA, not protein, is the genetic material in phages by using radioactive labeling.

Meselson-Stahl Experiment and the Semiconservative Model

The Meselson-Stahl experiment provided strong evidence for the semiconservative model of DNA replication.

• Semiconservative Replication: Each new DNA molecule consists of one parental strand and one newly synthesized strand.

• Experimental Design: Bacteria were grown in heavy nitrogen (15N) and then transferred to light nitrogen (14N). DNA was extracted after each generation and analyzed by density gradient centrifugation.

• Results: After one round of replication, DNA had intermediate density, supporting the semiconservative model.

Key Term: Semi-conservative replication means that each daughter DNA molecule contains one old (parental) strand and one new strand.

DNA Replication: Leading and Lagging Strands

DNA replication is a complex process involving multiple enzymes and proteins. The two strands are synthesized differently due to their antiparallel orientation.

• Leading Strand: Synthesized continuously in the 5' to 3' direction toward the replication fork.

• Lagging Strand: Synthesized discontinuously in short segments called Okazaki fragments, also in the 5' to 3' direction, but away from the replication fork.

• Okazaki Fragments: Short DNA fragments synthesized on the lagging strand, later joined by DNA ligase.

Comparison Table:

Feature	Leading Strand	Lagging Strand
Synthesis Direction	Toward replication fork	Away from replication fork
Mode of Synthesis	Continuous	Discontinuous (Okazaki fragments)
Primer Requirement	One primer needed	Multiple primers needed

DNA Replication Proteins and Their Functions

Several key proteins are involved in DNA replication, each with a specific role:

Protein/Enzyme	Function
Helicase	Unwinds the DNA double helix at the replication fork
Single-Stranded Binding Proteins (SSBPs)	Stabilize unwound DNA strands, preventing re-annealing
Topoisomerase	Relieves overwinding strain ahead of the replication fork
Primase	Synthesizes RNA primers to initiate DNA synthesis
DNA Polymerase III	Main enzyme that adds nucleotides to the growing DNA strand (5' to 3')
DNA Polymerase I	Removes RNA primers and replaces them with DNA nucleotides
DNA Ligase	Joins Okazaki fragments on the lagging strand

• Primer: A short RNA segment synthesized by primase, required to start DNA synthesis.

• Direction of Synthesis: New nucleotides are always added to the 3' end of the growing DNA strand.

DNA Repair Mechanisms

Cells have evolved several mechanisms to repair DNA damage and maintain genetic integrity.

• Nuclease: Enzyme that removes damaged or mismatched DNA segments.

• Nucleotide Excision Repair: Involves nuclease to excise damaged DNA, DNA polymerase to fill in the gap, and DNA ligase to seal the strand.

• Telomeres and Telomerase: The ends of linear DNA molecules are protected by repetitive sequences called telomeres. The enzyme telomerase extends telomeres, preventing loss of genetic information during replication.

Example: UV-induced thymine dimers are repaired by nucleotide excision repair.

Summary Table: DNA Replication Machinery

Order	Component	Task
1	Helicase	Unwinds DNA
2	SSBPs	Stabilize single strands
3	Topoisomerase	Relieves tension
4	Primase	Synthesizes RNA primer
5	DNA Polymerase III	Extends DNA strand
6	DNA Polymerase I	Replaces RNA primer with DNA
7	DNA Ligase	Joins DNA fragments

Key Equations and Concepts

• Direction of DNA Synthesis: $\text{DNA synthesis proceeds in the 5' \rightarrow 3' direction}$

• Base Pairing Rule: $\%A = \%T, \quad \%C = \%G$

Additional info:

• Mutations can arise from errors in replication or environmental damage; repair mechanisms are crucial for preventing genetic diseases.

• Practice questions and interactive resources are recommended for mastering these concepts.