DNA Replication and Gene Expression

Key Processes: DNA replication, transcription, and translation are fundamental processes in molecular biology that allow cellular function and inheritance.

Core Functions:
- Storage: DNA contains hereditary information.
- Replication: DNA must be accurately copied for cell division (DNA replication).
- Transcription: DNA is transcribed into mRNA to produce enzymes/structural proteins.
- Translation: mRNA is decoded to form proteins.
- Repair: The system must address and repair any damage to DNA.

Organisms: Two strains of Streptococcus pneumoniae.
- Smooth (S) strain: Pathogenic.
- Rough (R) strain: Non-pathogenic.
Procedure:
- Heat-killed S strain + live R strain introduced to a mouse.
Results:
- Mouse died, indicating transformation.
- Conclusions: A "transforming factor" from heat-killed S strain changed R strain to S strain.

Objective: Identify the transforming principle in Griffith's findings.
Observation: Highly purified extract containing DNA from heat-killed S strain could transform living R cells.
Experiments:
- Treated extract with various enzymes (DNases, RNases, Proteases).
Results:
- Only DNases destroyed transforming ability, confirming that DNA is the transforming principle.
Conclusion: DNA dictates cellular phenotype.

Bacteriophage T2: ID of genetic material.
Hypothesis: Protein or DNA must be the genetic material of T2.
Method:
- Label Bacteriophage DNA with radioactive phosphorus and proteins with radioactive sulfur.
Procedure: Infect E. coli with both labeled viruses.
- Separate phage capsids from infected cells.
Results:
- Radioactive phosphorus found in E. coli cells, confirming DNA as the genetic material.

Key Contributors: Rosalind Franklin, James Watson, Francis Crick.
Structure:
- Double-Helix: Consists of two strands coiled around each other.
- Nucleotides: Composed of a sugar (2-deoxyribose), a phosphate group, and nitrogenous bases.
- Base Pairing: A pairs with T, and G pairs with C via hydrogen bonding.
- Backbone: Formed from phosphodiester bonds connecting sugars and phosphates of adjacent nucleotides.
Exceptions: Organisms like D. radiodurans may have multiple genome copies.

Processes:
- DNA Replication → Transcription → Translation.
- Each step involves specific enzymatic actions and initiation/termination mechanisms.

Semiconservative Process: Each new DNA molecule consists of one old and one new strand.

Origin of replication: Specific starting points for DNA replication.
- Bacteria (E. coli) have a single origin (oriC).
Proteins Involved:
- DnaA binds to oriC, facilitating unwinding.
- DnaB (helicase) unzips DNA; DnaC (helicase loader) assists.
- DnaG (primase) lays down RNA primers essential for DNA polymerases.
- Single-stranded binding proteins prevent re-annealing of strands.

Leading and Lagging Strands:
- Leading strand synthesized continuously.
- Lagging strand synthesized in fragments (Okazaki fragments).
- DNA polymerase I removes RNA primers, filling gaps with nucleotides; DNA ligase seals the fragments.

In prokaryotes:
- Ends at specific termination sequences (ter sites) involving Tus proteins.
In eukaryotes:
- More complex as multiple origins are involved, with replication forks meeting.

Definition: Process where DNA is copied into RNA.
Initiation:
- Promoter: Start site for transcription.
- In bacteria, sigma factors direct RNA polymerase to the promoter.
- In eukaryotes, transcription factors first bind to the promoter, then recruit RNA polymerase.

In Bacteria:
- Rho-dependent: Presence of Rho protein.
- Rho-independent: RNA hairpin loop leads to dissociation.
In Eukaryotes: Depends on which RNA polymerase is involved.

Modifications made to pre-mRNA:
- Addition of 5' cap (7-methylguanosine).
- Addition of 3' poly(A) tail.
- Splicing: Removal of introns and joining of exons.

Definition: The process of decoding mRNA to synthesize proteins.
Mechanism:
- Ribosomes coordinate interactions with mRNA and tRNAs carrying amino acids.
- Codon-anticodon matching is crucial, with “wobble” allowing flexibility in pairing.

Folding: Proteins fold into their active forms aided by molecular chaperones.
Processing: Additional modifications like phosphorylation and glycosylation occur.
Transport: Proteins are directed to their functional locations using signal peptides.

General Overview: Mutations may not always be detrimental; they contribute to evolution and diversity.
Types of Mutations:
- Silent: No change in protein function.
- Missense: One amino acid is replaced by another.
- Nonsense: Introduction of a stop codon.
- Frameshift: Caused by insertions or deletions disrupting the reading frame.
Causes of Mutations:
- Spontaneous: Occur naturally at a low rate.
- Induced: Caused by environmental factors (e.g., chemicals, UV light).
- Example: Thymine dimers caused by UV exposure can lead to significant DNA alterations.

Understanding the fundamental processes of DNA replication, transcription, translation, and the effects of mutations provides insight into the mechanisms underlying genetic inheritance and expression, which are essential for all biological life.