Proteomics Lecture Notes

These flashcards cover key terms and definitions related to proteomics and protein analysis techniques, aimed at helping students understand and review the material in preparation for their exam.

The high-throughput study of proteomes, focusing on protein function, structure, and modifications, is called _.

Proteomics

Proteome

The dynamic set of all proteins expressed by a biological system, highly influenced by PTMs and cellular conditions.

Transcriptome

The complete set of RNA molecules (mainly mRNA) in a cell at a given time, serving as an intermediate between the genome and proteome.

Genome

The complete and relatively stable set of DNA sequences in an organism, containing all genetic instructions.

Dynamic

A characteristic describing transcriptomes and proteomes, which constantly change in response to stimuli, conditions, and cell type, unlike the static genome.

_ are covalent enzymatic modifications of proteins that regulate their activity, stability, and localization.

Post-translational modifications (PTMs)

Mass Spectrometry (MS)

An analytical technique measuring the mass-to-charge ratio (m/z) of ions to identify, quantify, sequence, and characterize PTMs of peptides and proteins.

Northern Blot

A technique used to detect and quantify specific mRNA levels in a sample via hybridization with a labeled probe.

RT-qPCR

A sensitive method for quantifying specific mRNA levels by converting RNA to cDNA, then amplifying and measuring with PCR.

Affinity purification

A chromatographic technique isolating specific proteins or complexes from mixtures by exploiting specific binding interactions.

Western Blot

A method combining electrophoresis and antibody detection to identify and quantify specific proteins based on their molecular weight.

Microarray

A high-throughput tool to simultaneously measure expression levels of thousands of genes (mRNAs) or detect genetic variations via hybridization.

RNA sequencing

A high-throughput sequencing technique revealing the quantity and sequences of all RNA molecules, providing insights into gene expression.

Reporter assays

Methods using a reporter gene (e.g., luciferase) linked to a regulatory element to measure transcriptional or post-transcriptional activity.

Cytosol

The aqueous part of the cytoplasm where many metabolic pathways, free ribosome protein synthesis, and early protein folding occur.

_ is a method separating proteins by molecular weight using SDS to give a uniform negative charge for gel electrophoresis.

SDS-PAGE

Ion exchange chromatography

A chromatography technique separating peptides and proteins based on their net charge by binding to an oppositely charged resin.

Reversed-phase liquid chromatography

A chromatography method separating peptides based on hydrophobicity by binding to a nonpolar stationary phase.

Tandem mass spectrometry (MS/MS)

A MS technique using two mass analyzers: one selects a precursor ion for fragmentation, and the second analyzes fragments to provide sequence information.

Peptide mass spectra

Graphs from MS showing relative abundance of peptide ions versus their mass-to-charge ratio (m/z), used for peptide identification.

Protein identification

The process of determining specific proteins in a sample by matching experimental peptide mass spectra to known protein databases.

The enzymatic attachment of carbohydrate side chains to proteins, influencing folding, stability, and cell recognition, is known as _.

Glycosylation

The covalent attachment of ubiquitin to a protein, often signaling for its degradation via the UPS, is called _.

Ubiquitination

Methylation

A PTM involving the addition of methyl groups to amino acid residues, important for gene regulation and protein function.

Acetylation

A PTM involving the enzymatic addition of acetyl groups to proteins, regulating function, stability, and often promoting gene transcription via histones.

Protein localization

The targeted distribution of proteins to specific subcellular compartments or the extracellular space, crucial for their function.

Protease

An enzyme that catalyzes the breakdown of proteins into smaller peptides or amino acids by cleaving peptide bonds.

_ is a serine protease that cleaves peptide bonds at the C-terminal side of lysine and arginine, used in proteomics.

Trypsin

Electrophoresis

A technique separating macromolecules (DNA, RNA, proteins) based on size and charge through a gel matrix in an electric field.

Protein synthesis

The cellular process of building proteins from genetic information, involving DNA transcription into mRNA and mRNA translation into an amino acid chain.

Mass spectrum

A plot showing the relative abundance of detected ions versus their mass-to-charge ratio (m/z) in MS experiments, used to infer molecular composition.

Affinity proteomics

A proteomics branch studying protein interactions or modification states by using affinity purification to isolate specific proteins and their partners.

Expression proteomics

The analysis of protein types and quantities, and how their expression levels change under various biological conditions or perturbations.

Synthesis of proteins

The cellular process from gene expression (DNA to mRNA, then mRNA to polypeptide) to protein folding and PTMs, resulting in functional proteins.

Cell signaling

The cellular communication process where cells receive, process, and transmit biochemical signals to elicit specific cellular responses.

Cell exterior

The extracellular environment around a cell where components like hormones, growth factors, and ECM interact with cell surface receptors.

Protein degradation

The regulated breakdown of proteins into smaller peptides or amino acids, crucial for quality control, removal of damaged proteins, and regulating protein abundance.

Biological properties

Inherent characteristics of proteins that determine their specific functions, such as enzymatic activity, binding specificity, and structural roles.

Gene expression

The multi-step process where genetic information is used to synthesize functional products (RNA or proteins), determining cell/organism traits.

High-throughput

An approach enabling rapid, automated analysis of a large number of samples or data points simultaneously, common in proteomics.

Complex protein mixtures

Samples containing a large, diverse array of proteins with varying abundances and PTMs, presenting significant analytical challenges.

Quantitative proteomics

A proteomics approach precisely measuring relative or absolute protein quantities to compare abundance changes across conditions.

Enzyme

A protein acting as a biological catalyst, significantly accelerating specific biochemical reactions by lowering activation energy.

Covalent bonding

A strong chemical bond formed by the sharing of electron pairs between atoms, fundamental for stable biomolecule structures.

Arbitrary units

A dimensionless scale used to express relative quantities or levels by comparing values against a reference, not an absolute physical quantity.

Mammalian cells

Eukaryotic cells from mammals, widely used in biomedical research due to physiological relevance and complex cellular machinery.

Statistical approaches

Mathematical methods used to analyze experimental data, especially in high-throughput studies, to assess variability, determine significance, and draw reliable conclusions.

Chromosomal DNA

The organized and compacted DNA molecules within chromosomes, carrying genetic information for heredity, often associated with histones.

ECM (Extracellular Matrix)

A complex network of secreted macromolecules outside cells, providing structural/biochemical support and influencing cell behavior.

Cell type

A category of cells sharing similar structure and performing specific functions, arising from differential gene expression.

Protein folding

The process where a polypeptide chain acquires its functional 3D structure, critical for its biological activity; misfolding can cause dysfunction.

Signal transduction pathways

A series of molecular events relaying and amplifying signals from a cell's environment to internal targets, leading to a coordinated cellular response.

Nature Reviews Molecular Cell Biology

A scientific journal publishing authoritative reviews and analyses in molecular and cell biology.

Sampling preparation

The critical initial stage in analytical workflows to obtain a representative biological sample for subsequent analysis (e.g., cell lysis, protein extraction).