Gene Ontology and Protein Functions Quiz

The linear sequence of amino acids in a protein chain, determined by the genetic code.

Local structures within a protein chain, formed by hydrogen bonds between backbone atoms. Alpha-helices and beta-sheets are common examples.

The overall three-dimensional structure of a protein, arising from interactions between amino acid side chains.

The structure formed when multiple protein chains (subunits) associate with each other.

The ability of an atom to exist in two mirror-image forms, like left and right hands.

A measure of the energy change associated with folding a protein. Determines whether folding is favorable or not.

The tendency of non-polar amino acid side chains to avoid contact with water, driving protein folding.

Weak interactions between atoms that are close together, playing a crucial role in protein structure and stability.

A method to quantify the likelihood of one residue being mutated from another in aligned sequences, representing the odds of a residue resisting mutation.

A matrix that represents the chemical properties of amino acid substitutions, with favorable scores for hydrophobic residues that are often observed.

A matrix derived from aligned sequences of protein families called BLOCKS, considering conserved blocks and ignoring loops, to amplify the signal of evolution.

A penalty applied to gaps (insertions or deletions) in protein alignments, calculated with an opening penalty and an extension penalty.

A common algorithm for sequence alignment that aims to find the best global alignment (matching entire sequences) by maximizing a similarity score.

Parts of a protein sequence that are evolutionarily distinct and often correspond to different homologous families, acting as the basic unit of evolution.

A specific type of sequence alignment that focuses on finding the most similar regions within two sequences, unlike global alignment which aligns the entire sequences.

A type of sequence alignment that aligns the entire sequences, finding the optimal match across the entire length of the sequences.

The largest number of residues from one sequence that can be matched with another, allowing for insertions and deletions (indels).

A 2-dimensional array where each cell represents a possible pairing of residues between two sequences.

A path through the alignment matrix, representing a possible alignment of two sequences. It reflects the insertion/deletion (indel) events chosen.

A numerical value assigned to each cell in the alignment matrix, representing the similarity or dissimilarity of the two residues. It determines how good a match is (high score) or bad (low score).

A dynamic programming method used to find the highest scoring local alignment between two sequences. It focuses on finding the best matching segments, regardless of overall length.

A technique used to compare a query sequence against a database of sequences to find similar sequences. It utilizes alignment algorithms to identify matches and infer homology, structure, and function.

A method that guarantees finding the highest scoring alignment for two given sequences using specific alignment scoring schemes. It also allows gaps, making it optimal for aligning sequences.

The biological function of a gene product, such as binding to a specific molecule or catalyzing a chemical reaction.

The overall biological process that a gene product contributes to, encompassing a series of events with a specific outcome.

The specific location within a cell where a gene product is active, such as a particular organelle or cellular compartment.

Indicates the level of confidence in a GO annotation, based on the type of evidence used.

A way to predict protein function by comparing a query sequence to a database of known protein sequences, identifying similar proteins likely sharing similar function.

Homologous proteins that arose from speciation events, having the same function in different species.

Homologous proteins that arose from gene duplication events within a species, potentially gaining new or modified functions.

A set of proteins or genes that share a common function or are involved in the same biological process, often identified based on their GO annotations.

The percentage of identical amino acids between two protein sequences.

A numerical classification system for enzymes based on their catalytic reaction, using four numbers separated by periods.

The process of determining the function of a protein based on its similarity to proteins with known functions.

A database that provides information about protein families and their domains.

A tool that identifies functional motifs and profiles within protein sequences.

A protein or molecule whose activity is modified to achieve therapeutic effects.

A small molecule identified through biological or computational screening with the desired effect (typically IC₅₀ ≤ 1 µM).

A chemically optimized version of a hit, designed to enhance therapeutic efficacy and minimize adverse effects, including toxicity and poor absorption.

The gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions.

The predicted Local Distance Difference Test (pLDDT) score measures the confidence of protein structure predictions, indicating the likelihood of a region being disordered.

These are functions predicted for Intrinsically Disordered Regions (IDRs) based on their characteristics. They include protein-binding, DNA-binding, RNA-binding, and linkers.

Clinical Phase I, II, and III are the three key phases of drug development, involving testing on humans to assess safety and efficacy.

This phase involves submitting data to regulatory bodies for approval of the drug's use and marketing.