Proteins -II

Flashcards covering protein folding, chaperones, denaturation, post-translational modifications (glycosylation, lipid modification, phosphorylation, other modifications), protein misfolding diseases (Alzheimer's, Cystic Fibrosis), and protein analysis techniques (purification, chromatography, electrophoresis, Western blot).

Protein folding (globular proteins)

The process where proteins fold to achieve maximum weak non-covalent interactions within the polypeptide chain, driven by thermodynamics to reach the least free energy state.

Chaperones

A group of proteins that assist protein folding in the cell under physiological and stress conditions, preventing aggregation and incorrect folding by stabilizing unfolded polypeptides.

Heat-shock proteins

A type of chaperone protein involved in assisting protein folding, especially under stress conditions.

Peptidyl-prolyl cis-trans isomerases (PPlase)

Enzymes that catalyze the interconversion of cis and trans isomers of peptide bonds involving proline residues, facilitating protein folding.

Protein-disulfide isomerases (PDI)

Enzymes that catalyze the formation, reduction, and isomerization of disulfide bonds, primarily in the endoplasmic reticulum, assisting in protein folding.

Protein denaturation

The loss of a protein's specific three-dimensional structure and function, caused by factors such as pH changes, temperature, chaotropic agents (e.g., urea), or detergents (e.g., SDS).

Post-translational modification (PTM)

The introduction of chemical groups onto a polypeptide chain after its translation from messenger RNA.

Glycosylation

A post-translational modification involving the enzymatic attachment of carbohydrates to proteins, forming glycoproteins.

O-linked glycoproteins

Glycoproteins where carbohydrates are attached via an ether linkage to the hydroxyl (-OH) group of serine (Ser) and threonine (Thr) residues, typically occurring in the Golgi apparatus.

N-linked glycoproteins

Glycoproteins where carbohydrates are attached via an amide linkage to the nitrogen (N) of asparagine (Asn) residues within a specific consensus sequence (Asn-X-Ser or Asn-X-Thr), mainly occurring in the endoplasmic reticulum.

Lipid modification

The attachment of lipid groups to a polypeptide chain after translation, forming lipoproteins.

Acetylation

A type of lipid modification involving the addition of an acetyl group to α- and ε-amino (NH2) groups of proteins.

Myristoylation

A lipid modification involving the covalent attachment of myristate (C14 fatty acid) to the N-terminal glycine via an amide linkage, influencing protein-protein and protein-lipid interactions and signal transduction.

Palmitoylation

A lipid modification involving the covalent attachment of palmitate (C16 fatty acid) to cysteine residues near the C-terminus via a thioester linkage, important for protein-protein interactions and membrane association.

Polyisoprenylation

A lipid modification where farnesyl pyrophosphate (C15) or geranylgeranyl pyrophosphate (C20) groups are attached to cysteine residues near the C-terminus, influencing protein-protein interactions and signal transduction.

GPI (glycosylphosphatidylinositol) anchor

A lipid modification found at the C-terminus of some membrane proteins, covalently linking them to the cell membrane through a glycosylated phosphatidylinositol molecule.

Phosphorylation

A dynamic and regulatory post-translational modification involving the transfer of a γ-phosphate group from ATP onto the hydroxyl (-OH) group of serine, threonine, or tyrosine residues by protein kinases.

Protein kinases

Enzymes that catalyze the phosphorylation of proteins by transferring a phosphate group from ATP to specific amino acid residues (serine, threonine, or tyrosine).

Ser/Thr kinases

Protein kinases that specifically phosphorylate the hydroxyl group of serine or threonine residues.

Tyr protein kinases

Protein kinases that specifically phosphorylate the hydroxyl group of tyrosine residues, often found in transmembrane proteins like growth factor receptors.

Hydroxylation

A post-translational modification involving the addition of a hydroxyl group, for example, to proline residues in collagen.

Sulfation

A post-translational modification involving the addition of a sulfate group, typically to tyrosine residues.

Ubiquitination

A post-translational modification involving the covalent attachment of ubiquitin, a small protein, to a target protein, often marking it for degradation or influencing its function (e.g., histones).

Sumoylation

A post-translational modification involving the covalent attachment of a Small Ubiquitin-like Modifier (SUMO) protein to a target protein, influencing its function or localization (e.g., histones).

Carboxylation

A post-translational modification involving the addition of a carboxyl group.

Misfolded protein

A protein that has failed to achieve its correct three-dimensional structure, which can lead to denaturation, partial loss of function, and be a cause of diseases.

Alzheimer's Disease (AD)

A neurological degenerative disease characterized by memory loss and confusion, linked to protein misfolding that results in dense brain plaques made of fibrillar β-amyloid proteins.

Cystic Fibrosis (CF)

A chronic disease affecting the lungs and pancreas, caused by protein misfolding of the cystic fibrosis transmembrane conductance regulator (CFTR) protein, often due to a deletion of phenylalanine at position 508.

Protein purification

The process of separating a specific protein of interest from a complex mixture of other proteins and molecules.

Gel filtration (Size-exclusion chromatography)

A protein purification method that separates proteins based on their molecular weight, where larger molecules elute first.

Ion-exchange chromatography

A protein purification method that separates proteins based on their net electrical charge at a given pH, utilizing charged resins.

Hydrophobic interaction chromatography

A protein purification method that separates proteins based on their hydrophobicity, typically by binding in high salt concentrations and eluting in lower salt concentrations.

Affinity interaction chromatography

A highly specific protein purification method that separates proteins based on their unique affinity for specific substrates, ligands, or antibodies immobilized on a matrix.

SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis)

An electrophoresis technique where proteins are denatured by SDS and separate primarily based on their molecular size, with smaller polypeptides migrating faster.

Native PAGE

An electrophoresis technique performed without SDS, where proteins separate based on both their size and native charge, maintaining their folded structure.

2D gel electrophoresis

A protein separation technique combining isoelectric focusing (separating by pI/charge) in the first dimension and SDS-PAGE (separating by size) in the second dimension, allowing high-resolution separation.

Isoelectric focusing (IEF)

The first dimension of 2D gel electrophoresis, where proteins separate based on their isoelectric point (pI), the pH at which their net charge is zero.

Western blot

A technique that follows SDS-PAGE by transferring separated proteins onto a membrane, then detecting a specific protein of interest using primary and secondary antibodies.