Bio 111 - Lab 5 Bioinformics II

Bioinformatics

The use of computers, software, and mathematical models to process and integrate biological information from large data sets.

Genomics

The study of entire genomes, including the complete set of genes, nucleotide sequences, organization, and species interactions.

Proteome

The entire set of proteins produced by a specific cell type, tissue, or organism.

Gel Electrophoresis Principle

Technique using electrical current to separate DNA fragments in an agarose gel based on molecular size and negative electrical charge.

Agarose Gel Matrix

A polymeric mesh through which smaller DNA fragments migrate faster and farther toward the positive anode (+).

DNA Electrical Charge & Migration Direction

DNA is negatively charged (due to its phosphate backbone) and moves from the negative electrode (cathode, -) toward the positive electrode (anode, +).

Homozygous STR Banding

An individual with two identical STR allele repeat lengths exhibits 1 single band on an agarose gel.

Heterozygous STR Banding

An individual with two different STR allele repeat lengths exhibits 2 distinct bands on an agarose gel.

Minimum & Maximum Bands for 3 STR Loci

Minimum = 3 bands (all loci homozygous); Maximum = 6 bands (all loci heterozygous).

Gel Electrophoresis Sample Loading

10 uL total (6.5 uL PCR product + 3.5 uL loading buffer) loaded into wells located at the negative (-) end of the chamber.

Central Dogma of Molecular Biology

DNA -> (Transcription) -> mRNA -> (Translation) -> Protein.

Transcription

The cellular process in which RNA polymerase synthesizes a complementary mRNA mobile copy from a DNA template.

Translation

The ribosomal process converting mRNA nucleotide triplet codons into an amino acid polypeptide chain.

Amino Acid General Structure

An amino group (NH3+), a carboxyl group (COO-), a central carbon, and a variable side chain (R-group) determining chemical properties.

Degeneracy of Genetic Code

Feature where a single amino acid can be specified by more than one triplet codon (e.g., AUC and AUA both code for isoleucine).

Start Codon

AUG (codes for Methionine), which establishes the translation reading frame near the 5' end of mRNA.

Stop / Nonsense Codons

The 3 codons (UAA, UAG, UGA) out of 64 that signal the termination of protein translation.

Silent Mutation

A point mutation substituting a nucleotide base that does not change the resulting amino acid sequence.

Missense Mutation

A point mutation substituting a nucleotide base that changes one amino acid to another in the protein chain.

Nonsense Mutation

A point mutation substituting a nucleotide base that prematurely converts an amino acid codon into a stop codon.

Frameshift Mutation

An insertion or deletion of 1 or 2 nucleotides that shifts the mRNA triplet reading frame for all downstream codons.

Phylogenetic Tree

A diagram representing a hypothesis of evolutionary relationships among species based on genetic or physical traits.

Branch Point (Node)

An internal point on a phylogenetic tree representing an ancestral divergence event into distinct lineages.

Branch Length

Component of a phylogenetic tree proportional to the elapsed evolutionary time or genetic change since a split.

Sister Taxa

Two lineages that stem directly from the same immediate branch point (node).

Basal Taxon

A lineage that evolved early from the root of a tree and remains unbranched near the base.

Polytomy

A branch point on a phylogenetic tree from which more than two descendant groups emerge.

Sequence Alignment

The process of lining up nucleotide or protein sequences to identify regions of similarity, mutations, and insertions/deletions.

MEGA Software

Molecular Evolutionary Genetics Analysis software used to align sequences, translate codons, and construct phylogenetic trees.

Calculating Band Size (Rate of Change)

Rate of Change = (Difference in bp between ladder bands) / (Distance in cm between ladder bands).

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