Gene Editing and Molecular Biology Overview

Selective Breeding vs. Gene Editing

Selective breeding manipulates existing genetic variation within a population to enhance desirable traits, through controlled mating
Gene editing directly modifies the genome by adding, deleting, or changing DNA sequences at a precise location, offering more precise and targeted alterations

Endogenous DNA Replication and Repair Enzymes in Gene Editing

Enzymes involved in DNA replication and repair, like nucleases and polymerases, are utilized in gene editing to introduce or repair DNA alterations.
These enzymes may be harnessed or modified for targeted DNA modifications in gene editing technologies.

Molecular Cloning Steps

Isolation of DNA fragment of interest
Insertion of the fragment into a vector (e.g., plasmid)
Introduction of the recombinant vector into a host organism (transformation)
Selection of transformed host cells
Amplification of the target DNA in the host organism

PCR DNA Amplification

PCR uses heat to denature DNA, followed by annealing of primers to the DNA, and extension by DNA polymerase to make additional copies.
Multiple cycles amplify the DNA exponentially, producing millions of copies.

DNA Separation by Gel Electrophoresis

DNA fragments migrate through a gel matrix under an electric field, with smaller fragments moving faster
This creates a separation pattern allowing visualization and analysis of different DNA sizes.

CRISPR/Cas9 Gene Editing

CRISPR/Cas9 uses a guide RNA to target a specific DNA sequence
Cas9 enzyme makes a double-strand break in the DNA
Cell's own DNA repair mechanisms incorporate desired alterations

Potential Impacts of Gene Editing

Ethical considerations regarding human gene editing require careful societal dialogue and regulation.
Gene editing holds promising applications for treating genetic diseases, enhancing crop yields, and understanding biological processes. This can have huge implications for society and the environment, but requires careful consideration of potential downsides.

Major Components of Genomics

Genome sequencing, annotation, and comparison are key elements
Also includes studying interactions between genes and the environment.

Genetic vs. Physical Maps

Genetic maps: based on recombination frequency, measure relative distances between genes.
Physical maps: based on physical distances along the DNA, use base pair measurements.
Example: Genetic: Position of a gene relative to other genes. Physical: exact base-pair location of a gene.

DNA Sequencing Methods

Automated sequencing uses fluorescently labeled nucleotides to determine sequence, simplifying and accelerating the process.
Next-generation sequencing (NGS) enables massively parallel sequencing, facilitating high-throughput data generation.

Clone-Contig vs Shotgun Sequencing

Clone-contig sequencing: relies on assembling overlapping DNA fragments from clones.
Shotgun method: determines many overlapping fragments, with software aligning them computationally to assemble the whole genome.

Genome Annotation Importance

Genome annotation assigns functions to DNA sequences, providing crucial links for understanding genes, regulatory elements, and other functional regions.

Non-coding DNA Roles

Non-coding DNA regions play diverse roles in gene regulation and other biological processes.

Comparative Genomics, Functional Genomics, and Proteomics

Comparative genomics: comparing genomes of different species
Functional genomics: predicting and studying gene functions
Proteomics: studying entire sets of proteins produced in an organism

Genomics Applications

Genomics is used in diverse fields like medicine (disease diagnosis and treatment) and agriculture (producing improved crops) and various biotechnological uses.

Automated Sequencing and other key terms

Automated methods use fluorescent labels to analyze sequence data.
Base pairs: fundamental units of genetic information.
Bioinformatics: uses computational tools to analyze biological data.
BLAST (Basic Local Alignment Search Tool): compares sequences to identify similarities.
Chain-terminating nucleotides: used in Sanger sequencing, stopping DNA synthesis.
Chromosome maps: visual representation of genes.
Clone-contig method: using clones to obtain larger DNA fragments.
Coding DNA: gene-coding regions.
Comparative Genomics: comparing genomes of different species.
Dideoxynucleotides: prevent further DNA synthesis.
DNA microarray: analyzes gene expression patterns.
Encylopedia Of DNA Elements (ENCODE): research on the function of non-coding DNA
Functional Genomics: understanding gene functions.
GenBank: online database of genetic sequences.
Genetic Map: visual mapping of genes based on location.
Genomics: the study of genomes.
Human Genome Project: sequencing the human genome.
Kilobase pairs: units of measure, 1000 base pairs.
Mass Spectrometry: identifying proteins and mass-based analysis.
Next-Generation Sequencing: high-throughput genome sequencing.
Non-coding DNA: regions outside of protein-coding genes.
Open Reading Frame (ORF): region in a sequence that could potentially code for a protein.
Physical Map: physical distance between genetic markers.
Protein Microarrays: measuring protein levels and interactions.
Proteome: complete protein content of an organism.
Proteomics: study of proteins.
Pseudogenes: non-functional genes.
Restriction Maps: locating restriction sites in DNA.
Segmental Duplications: extensive duplication of segments within a genome.
Sequence-tagged site (STS): short, distinctive DNA sequence used as markers
Shotgun method: using small fragments to assemble a genome.
Simple Sequence Repeats (SSRs): short repeating DNA sequences
Structural DNA: DNA involved in chromosome structure.
Synteny: conserved order of genes across different species
Synthetic biology: designs biological systems
Transcriptome: all RNA molecules in a cell or organism
Transposable elements: mobile DNA sequences