Molecular Evolution and Bioinformatics Flashcards

Vocabulary practice flashcards covering the molecular basis of evolution, sequence alignment, nucleotide substitution models, phylogenetic tree reconstruction, biological databases, DNA barcoding, and molecular biology laboratory protocols.

Phosphodiester Linkage

A covalent linkage connecting the $5^\prime$-phosphate group of one nucleotide to the $3^\prime\text{-OH}$ group of an adjoining nucleotide in a nucleic acid strand.

Central Dogma

The framework describing the flow of genetic information: DNA replicates itself, is transcribed into RNA, and RNA is translated into protein.

Weismann's Barrier

The principle of germline continuity and isolation, stating that hereditary information passes intact from parent to offspring and somatic changes cannot be transmitted into hereditary information.

Operon

A cluster of structural genes transcribed under a single promoter and regulated by a common operator.

Open Reading Frame (ORF)

A continuous portion of DNA that is translated into amino acids and contains no stop codons.

Pseudogene

A DNA segment that exhibits high sequence similarity to a functional gene but carries defects preventing its proper expression.

Base Selection

A DNA replication fidelity mechanism in which the correct incoming base causes a conformational change that engages the polymerase active site ($5^\prime \rightarrow 3^\prime$), while an incorrect base fails to close the enzyme.

Proofreading

An error-correction mechanism in DNA polymerases where an incorrect base distorts the helix and swings into the exonuclease site to be excised in the $3^\prime \rightarrow 5^\prime$ direction before synthesis continues.

Post-replication Repair

A repair mechanism that detects helical bulges caused by mismatched bases, distinguishes the newly synthesized strand by targeting the unmethylated strand, and excises and replaces the faulty segment.

Silent Mutation

A synonymous point mutation in a coding region that alters a codon without changing the encoded amino acid.

Noisy Synonymous Mutation

A synonymous substitution that does not change the amino acid sequence but alters RNA processing, such as disrupting a splice junction (as seen in $\beta^+\text{-thalassemia}$).

Missense Mutation

A nonsynonymous point mutation in which a single base substitution results in a codon that specifies a different amino acid.

Nonsense Mutation

A nonsynonymous point mutation that converts an amino acid codon into a premature stop codon, terminating translation early.

Photoreactivation

The first repair pathway for UV-induced damage that directly reverses thymine dimers back to the original sequence without introducing mutations.

SOS Response

An error-prone fourth repair pathway for severe UV-induced damage that incorporates incorrect nucleotides, resulting in imperfect repair (mutations) or failure to repair leading to cell death.

Single Nucleotide Polymorphism (SNP)

A variation at a single base pair position in the genome among individuals within a population.

Taq Polymerase

A heat-stable DNA polymerase derived from the extremophilic bacterium Thermus aquaticus, originally discovered in Yellowstone National Park hot springs, used to amplify DNA in PCR.

Homology

Similarity between traits, structures, or sequences that is inherited directly from a common ancestor.

Homoplasy (Analogy)

Structural or sequence similarity between organisms that arose independently through convergent evolution rather than through common descent.

Pairwise Sequence Alignment

The direct, position-by-position comparison of two sequences to determine matches, mismatches, and gaps.

Multiple Sequence Alignment (MSA)

The simultaneous alignment of three or more sequences used to identify conserved regions, predict secondary structures, and infer evolutionary relationships.

Local Alignment

An alignment strategy that identifies islands of high similarity between sequences of varying lengths, commonly utilized in database search tools such as BLAST.

Global Alignment

An alignment approach that computes the optimal match across the entire length of sequences, best suited for sequences of similar length and high homology.

Indel

An insertion or deletion event within a sequence, represented as a gap character (-) in a sequence alignment.

Jukes and Cantor (1969) Model

A one-parameter nucleotide substitution model assuming all substitution types occur at an equal rate ($\alpha$) without directional bias, where the probability of a base remaining unchanged over one unit of time is $P_A(1) = 1 - 3\alpha$.

Kimura (1980) Two-Parameter Model

A nucleotide substitution model that assigns different rates to transitions ($\alpha$) and transversions ($\beta$), yielding an unchanged nucleotide probability of $P_{AA}(1) = 1 - \alpha - 2\beta$.

PAM Matrices

Point Accepted Mutation matrices based on closely related protein sequences, where 1 PAM unit corresponds to 1 amino acid change per 100 residues.

BLOSUM Matrices

Blocks Substitution Matrices derived directly from local, ungapped alignment blocks of diverse protein families, with numeric suffixes indicating the sequence identity threshold used for clustering (e.g., BLOSUM62).

Gap Opening Penalty

The numerical penalty assessed for initiating a new gap of one residue in a sequence alignment.

Gap Extension Penalty

The incremental cost assessed for extending an existing gap by each additional nucleotide or amino acid.

Plesiomorphy

An ancestral or primitive character state existing prior to the evolutionary divergence of the taxa being studied.

Apomorphy

A derived character state representing an evolutionary novelty relative to the ancestral state.

Autapomorphy

A derived character state unique to a single terminal taxon within a phylogenetic tree.

Synapomorphy

A shared derived character state that unites two or more lineages and provides evidence of common ancestry.

ClustalW

A progressive multiple sequence alignment tool that computes pairwise similarity scores, builds a guide tree, and aligns sequences sequentially.

MUSCLE

Multiple Sequence Comparison by Log-Expectation; a multiple sequence alignment program designed to achieve superior accuracy and speed compared to ClustalW.

Molecular Phylogenetics

The study of evolutionary relationships among organisms using molecular data (DNA, RNA, proteins) in combination with statistical and computational techniques.

Operational Taxonomic Unit (OTU)

A terminal node or tip on a phylogenetic tree that represents the actual sampled biological data being evaluated (species, strain, or sequence).

Hypothetical Taxonomic Unit (HTU)

An internal node on a phylogenetic tree representing an inferred ancestral taxon or sequence.

Hard Polytomy

A multifurcating internal node with three or more descendent branches representing true, simultaneous divergence of taxa.

Soft Polytomy

A multifurcating node representing uncertainty or an inability to unambiguously determine branch order with the available data.

Cladogram

An unscaled phylogenetic tree where branch lengths are arbitrary and indicate only the relative recency of common ancestry.

Phylogram

A scaled phylogenetic tree where the lengths of branches are explicitly proportional to the amount of evolutionary change or number of substitutions.

Newick Format

A standardized computer text format that represents phylogenetic tree topologies using nested parentheses enclosing comma-separated taxon labels.

Monophyletic Group

A phylogenetic clade that includes an ancestral taxon and all of its descendants.

Paraphyletic Group

A phylogenetic group that includes an ancestral taxon and some, but not all, of its descendants (e.g., traditional reptiles excluding birds).

Polyphyletic Group

A group of organisms that does not include the common ancestor of all of its members.

Orthologs

Homologous genes in different species that separated as a result of a speciation event.

Paralogs

Homologous genes that arose via gene duplication within a single genome.

Xenologs

Homologous genes that have been acquired through horizontal gene transfer across taxa.

UPGMA

Unweighted Pair Group Method with Arithmetic Mean; a distance-based clustering method that assumes a constant molecular clock rate to generate an ultrametric tree.

Maximum Parsimony

A character-based phylogenetic method that chooses the tree topology requiring the minimum total number of character state transitions (shortest Tree Length).

Long-Branch Attraction

A systematic artifact in phylogenetic analysis where rapidly evolving or highly divergent lineages artificially cluster together regardless of true relationship.

Branch and Bound

An exact search algorithm for maximum parsimony that guarantees finding the optimal tree without evaluating every possible tree by abandoning paths exceeding the current upper bound; practical for up to 20 taxa.

Maximum Likelihood (Phylogenetics)

A statistical phylogenetic method that finds the tree topology and branch lengths that maximize the conditional probability of producing the observed dataset under a specific model of sequence evolution ($L = P(\text{data} \mid \text{tree})$).

Bootstrap Technique

A statistical resampling method that samples alignment columns with replacement to produce pseudoreplicate datasets, determining percentage support for specific nodes in the tree.

Strict Consensus Tree

A summary tree generated from multiple equally optimal trees that retains only nodes found in 100% of the candidate trees, collapsing all conflicting branches into polytomies.

Majority-Rule Consensus Tree

A consensus tree that retains branches that appear in at least a specified percentage (typically $\ge 50\%$) of candidate trees.

Outgroup Rooting

The standard method of rooting a phylogenetic tree using one or more taxa known to be phylogenetically outside the group of interest.

Archival Database

A primary biological database that stores directly submitted, raw experimental data, such as nucleotide and protein sequences, SNP catalogs, or metabolic pathways.

Derived Database

A secondary database containing computationally inferred information, motifs, classifications, or connections curated from analyzing archival data.

INSDC

The International Nucleotide Sequence Database Collaboration, a consortium uniting NCBI GenBank, ENA/EBI, and DDBJ to ensure global access and synchronization of nucleotide sequence data.

DNA Barcoding

A taxonomic method that identifies biological species using a standardized, short diagnostic DNA sequence fragment.

Sanger Sequencing

A sequencing technique that targets a specific DNA region using an oligonucleotide sequencing primer binding adjacent to the region of interest to determine nucleotide sequence.

Buffer ATL

A lysis buffer used in DNA extraction that breaks open cells and disrupts cellular membranes.

Proteinase K

A protease enzyme added during the lysis step of DNA extraction to digest proteins and inactivate nucleases.

Buffer AL

A lysis/binding reagent combined with ethanol in DNA extraction to establish chemical conditions favoring DNA binding to a silica spin column membrane.

Buffer AE

An elution buffer that releases purified DNA from the silica membrane of a spin column into solution.

Qubit Fluorometer Assay

A target-specific quantitation method that measures DNA concentration via fluorescence emitted by a dye selectively bound to DNA, calibrated using blank and known concentration standards.

Melting Temperature ($T_m$)

The temperature at which 50% of primer molecules are annealed to their complementary template strand and 50% are denatured in solution.

GC Clamp

The inclusion of 1 to 3 G or C bases at the $3^\prime$ terminus of a PCR primer to strengthen binding at the initiation site of DNA polymerase extension.

Agarose Gel Electrophoresis

A laboratory method that separates negatively charged nucleic acid fragments through a porous agarose matrix toward a positive electrode at speeds inversely proportional to molecular size.

Sodium Dodecyl Sulfate (SDS)

An anionic detergent added to proteins before gel electrophoresis that denatures them into linear polypeptides and imparts a uniform negative charge.

DNA Ladder

A molecular weight standard consisting of DNA fragments of known lengths run alongside samples during gel electrophoresis to estimate the size of amplified PCR products.

Negative Control (PCR)

A PCR reaction containing all reagents except the template DNA, utilized to detect reagent contamination; expected to show no amplification bands.