PHARS8033 - Genomics and Bioinformatics Flashcards

Flashcards covering key vocabulary terms from the PHARS8033 Genomics and Bioinformatics Lab 1: Gene Identification and Primer Design lecture notes, including bioinformatics tools, genomic elements, primer properties, and experimental procedures.

Ensembl

A bioinformatics database and tool used for exploring genomics, genes, and transcripts across various species.

NCBI

National Center for Biotechnology Information, a major bioinformatics resource and database used for gene identification, sequence data, and more.

Oligocalc

An online tool used to analyze primer properties like GC content, melting temperature (Tm), and predicted secondary structures.

Primer3Plus

A web-based tool for automatically designing PCR primer pairs based on user-defined target regions and parameters.

Model Organisms

Organisms (e.g., mouse, rat, zebrafish) used in research due to ethical feasibility, genetic similarity to humans, and well-characterized biology.

Tmem179

The specific human gene (transmembrane protein 179) used as an example for gene identification and primer design in the lab.

Transcript

An RNA copy produced from a gene, which can be protein-coding or non-coding.

Gene Structure

The organization of a gene including its exons (coding regions) and introns (non-coding regions).

Exons

The coding regions of a gene that are retained in the mature mRNA and translated into protein.

Introns

The non-coding regions within a gene that are removed during RNA splicing and not present in mature mRNA.

FASTA format

A text-based format for representing nucleotide or amino acid sequences, typically starting with a header line followed by the sequence data.

gDNA (Genomic DNA) sequence

The complete DNA sequence of a gene including promoter regions, non-coding DNA, coding DNA (cDNA), introns, and exons for all transcripts.

cDNA (coding DNA) sequence

The DNA sequence representing the mature mRNA after splicing, containing only the exons.

Gene Record

A central page in databases like NCBI that provides comprehensive information about a specific gene, including its summary, genomic context, and transcripts.

Orthologs

Genes in different species that evolved from a common ancestral gene by speciation and typically retain the same function.

Accession Number

A unique identifier assigned to a specific sequence entry in a database, indicating its type and version.

NM_ prefix

Prefix for a curated, validated coding mRNA sequence record in NCBI's RefSeq database.

NR_ prefix

Prefix for a curated non-protein-coding RNA sequence record in NCBI's RefSeq database.

NP_ prefix

Prefix for a protein product translation derived from an NM_ mRNA record in NCBI's RefSeq database.

XM_ prefix

Prefix for a computationally predicted mRNA sequence model.

XP_ prefix

Prefix for a computationally predicted protein product translated from an XM_ mRNA record.

Conserved Domains

Functional regions within a protein sequence that are often maintained across different species, indicating specific biological roles.

Structure database (MMDB)

A database containing experimentally determined 3D protein structures (e.g., from X-ray crystallography or NMR).

Tissue Expression section

A section in gene records providing data on where and how much a gene is expressed across various tissues.

GTEx (Genotype-Tissue Expression) project

A large-scale project that provides baseline gene expression levels across dozens of normal human tissues.

TPM (Transcripts Per Million)

A normalized unit used to measure gene expression levels, allowing for comparison between different tissues or samples.

gDNA PCR

Polymerase Chain Reaction designed to amplify a specific region of genomic DNA.

Target Amplicon

The specific region of DNA that is intended to be amplified by PCR.

Forward Primer (Fw)

A short, synthetic oligonucleotide designed to bind to the upstream exon of a target sequence for PCR amplification.

Reverse Primer (Rv)

A short, synthetic oligonucleotide designed to bind to the downstream exon on the sense strand of a target sequence, and whose reverse complement forms the actual primer for PCR amplification.

Reverse-complement

The sequence derived by reversing a DNA strand's sequence and then complementing each base (A with T, G with C); essential for designing reverse primers.

Primer Length

The number of nucleotides in a primer, ideally between 18-22 base pairs.

GC Content

The percentage of Guanine and Cytosine bases in a DNA sequence, an important factor for primer melting temperature (ideal 40-60%).

Melting Temperature (Tm)

The temperature at which half of the DNA strands in a double helix denature into single strands; a critical property for primer annealing (ideal within 5°C MAX, 2°C Optimal difference between primers).

Secondary Structures (Primer)

Unintended structures like hairpins that a single primer molecule can form, potentially preventing it from binding to its target DNA.

ΔG (Gibbs Free Energy)

A thermodynamic value indicating the stability of a secondary structure; a more negative value suggests a more stable and potentially problematic structure.

Primer-Dimer Formation

The undesirable binding of a forward primer to a reverse primer (or two of the same primer) instead of the target DNA, which can inhibit PCR efficiency.

Amplicon Size

The total length in base pairs of the DNA product amplified by a primer pair in PCR.

Agarose Gel Electrophoresis

A laboratory technique used to separate DNA fragments by size, typically for visualizing PCR products.

Target Coordinates

Specific base pair numbers entered into primer design software (like Primer3Plus) to define the region of the sequence from which primers should amplify.

Specificity Check

A process or software feature that verifies if primers are predicted to bind only to the intended target region and not to other non-specific locations in the genome.