DNA Replication, Gene Expression, Mutations, and Molecular Genetics Techniques

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Nucleotides are the building blocks of DNA, each consisting of a phosphate group, a deoxyribose sugar, and a nitrogenous base (adenine, thymine, cytosine, or guanine).
DNA is a double helix formed by two antiparallel strands held together by hydrogen bonds between complementary bases (A-T and G-C).
The 5’ end of a DNA strand has a free phosphate group, while the 3’ end has a free hydroxyl group.
Base pairing: A pairs with T (2 hydrogen bonds), G pairs with C (3 hydrogen bonds).

DNA replication is the process by which a cell copies its DNA before cell division.
It is semiconservative: each new DNA molecule consists of one parental and one newly synthesized strand.
Replication begins at specific sites called origins of replication.

The leading strand is synthesized continuously in the 5’ to 3’ direction.
The lagging strand is synthesized discontinuously, forming short segments called Okazaki fragments, which are later joined by DNA ligase.

DNA polymerase: Synthesizes new DNA strands by adding nucleotides to the 3’ end.
Helicase: Unwinds the DNA double helix.
Primase: Synthesizes RNA primers to initiate DNA synthesis.
Ligase: Joins Okazaki fragments on the lagging strand.
Single-strand binding proteins: Stabilize unwound DNA.

Transcription is the synthesis of RNA from a DNA template, initiated at the promoter region.
RNA polymerase binds to the promoter and synthesizes RNA in the 5’ to 3’ direction.
Eukaryotic mRNA processing includes addition of a 5’ cap, poly(A) tail at the 3’ end, and removal of introns (non-coding regions), leaving only exons (coding regions).

Translation is the process by which ribosomes synthesize proteins using mRNA as a template.
The start codon (AUG) signals the beginning of translation; stop codons (UAA, UAG, UGA) signal termination.
Codons are three-nucleotide sequences on mRNA that specify amino acids; anticodons are complementary sequences on tRNA molecules.
Polycistronic mRNA (common in prokaryotes) encodes multiple proteins; monocistronic mRNA (common in eukaryotes) encodes a single protein.

Genotype: The genetic makeup of an organism (the sequence of DNA).
Phenotype: The observable characteristics or traits resulting from the genotype.

A mutation is a heritable change in the DNA sequence.
Mutagens are physical or chemical agents that increase the mutation rate (e.g., UV rays, chemicals).
UV radiation can cause thymine dimers, leading to errors during DNA replication.

Point mutations: Change in a single nucleotide (e.g., substitution).
Insertions and deletions: Addition or loss of nucleotides, which may cause frameshifts.
Silent, missense, and nonsense mutations: Affect the resulting protein differently.

Plasmids are small, circular, double-stranded DNA molecules found in bacteria, independent of the chromosomal DNA.
They replicate from a specific origin of replication (ori), allowing them to multiply independently.

Transformation is the uptake of naked DNA (often plasmids) from the environment by a bacterial cell.

Conjugation is the transfer of genetic material between bacteria via direct contact, often mediated by a pilus (a tube-like structure).
The pilus facilitates the transfer of plasmids from donor to recipient cells.

Transduction is the transfer of bacterial genes by viruses (bacteriophages).
Viruses can accidentally package bacterial DNA and transfer it to another bacterium.

Replica plating is a technique used to transfer colonies from one agar plate to another, preserving the spatial arrangement, to identify mutants or select for specific traits.

PCR is a technique used to amplify specific DNA sequences in vitro.
Principles of PCR:
- Denaturation: DNA strands are separated by heating.
- Annealing: Primers bind to target sequences.
- Extension: DNA polymerase synthesizes new DNA strands.
Usefulness of PCR: Used in diagnostics, cloning, forensics, and research to detect and amplify DNA.
Key equation:

Where is the number of DNA molecules after cycles, starting from molecules.

A microarray is a laboratory tool used to detect the expression of thousands of genes at once by hybridizing labeled cDNA to a grid of DNA probes.
Applications include gene expression profiling, mutation analysis, and comparative genomics.

Method	Description	Key Features
Transformation	Uptake of naked DNA from environment	Competent cells, plasmid uptake
Conjugation	Direct transfer of DNA via cell-to-cell contact	Pilus formation, plasmid transfer
Transduction	Transfer of DNA by bacteriophage (virus)	Generalized or specialized, virus-mediated

Some details (e.g., specific enzymes, types of mutations) were expanded for academic completeness.
For more in-depth study, refer to textbook chapters on DNA replication, gene expression, and microbial genetics.