Lec 3 Post-Translational Modifications

Size: 0.1-10 μm
**Components: **
- Plasma membrane
- Cytoplasm
- DNA (located in the nucleoid region)
- Ribosomes

Key Concepts:
- Cell: Basic structural, functional unit of all living organisms.
- Genome: Complete set of genes or genetic material present in a cell.
- Transcription: Process of copying a segment of DNA into RNA.
- Translation: Process of interpreting the RNA to synthesize proteins.
- Post-translational modification: Chemical changes to the protein following translation.
- Transcriptome: The complete set of RNA transcripts produced at any one time.
- Proteome: The entire set of proteins expressed by a genome, cell, tissue, or organism.

Overview:
- Over 650 types of known PTMs.
- PTMs fall into three broad categories:
1. Cleavage of amino acid chains
2. Addition of molecules (e.g., lipids, carbohydrates, functional groups)
3. Formation of cross-linkages (e.g., addition of disulphide bonds)
Function: PTMs help to achieve proper protein folding into its tertiary structure.

PTMs can occur at any stage of the protein lifecycle.
- Frequently modify proteins shortly after translation to ensure correct folding or proper localization (e.g., to the membrane).
- Other modifications may occur after folding for the activation/deactivation of enzymatic activity.
- Proteins can be covalently linked to tags for degradation.
PTMs typically occur at specific amino acid side chains or peptide linkages and are mediated by enzymes such as kinases, phosphatases, transferases, and ligases.

Carbamylation, Methylation: Involves modification of side chains of amino acids like Lysine (Lys), Arginine (Arg), and others.
Phosphorylation: Typically occurs on residues of Serine, Threonine, or Tyrosine.
Ubiquitination: A type of modification often involving lysine residues that tags proteins for degradation or functional changes.
SUMOylation: Attachment of small ubiquitin-like modifiers to lysine residues in proteins.
Glycosylation: Addition of carbohydrate moieties to proteins, altering solubility and imparting stability against proteolytic degradation.

PTMs are critical for enabling protein functions and coordinating cellular processes such as:
- Cell cycle
- Differentiation
- Metabolism
Clinical Relevance: Defects in PTMs are linked to various diseases, such as Tau hyperphosphorylation in Alzheimer's Disease.

Process: Mediated by protein kinases which add phosphate groups to specific amino acid residues.
Key Amino Acids: Primarily involves Serine, Threonine, and Tyrosine.
Effects: Modifies protein activity, facilitating interactions between molecules and thereby regulating cellular activities.
Dephosphorylation: Period of protein inactivation mediated by phosphatases.

Definition: Covalent attachment of carbohydrate units (glycans) to proteins during their synthesis.
Location: Occurs mainly in the Endoplasmic Reticulum (ER) and Golgi apparatus.
Types of Glycosylation:
- N-linked: Glycans attached to asparagine residues.
- O-linked: Glycans attached to the hydroxyl group of serine or threonine residues.
Functionality: Glycosylation plays roles in stability, signaling, and cell interaction.

Glycosylation affects:
- Protein solubility
- Resistance to proteolysis
- Biological activity
- Antigenic properties
Prokaryotic vs. Eukaryotic Systems: Prokaryotes like E. coli produce forms that are less usable without refolding post-extraction; eukaryotic systems (e.g., CHO cells) may add human-like glycoforms.

Overview: Involves binding a small protein (ubiquitin) to a target protein, altering its fate.
Mechanism: Involves three enzymes:
1. E1: Ubiquitin-activating enzyme
2. E2: Ubiquitin-conjugating enzyme
3. E3: Ubiquitin-ligase enzyme
Outcomes: Ubiquitinated proteins are tagged for degradation via the proteasome.
Reversibility: Removal of ubiquitin is managed by deubiquitinases (DUBs).

Monoubiquitination: A single ubiquitin molecule added to a protein.
Polyubiquitination: Multiple ubiquitins attached, forming chains.
- Different chains: e.g., K48, K63, K11 chains for different cellular signaling functions.

Types: Includes arginine and lysine methylation.
Enzymes: Arginine methyltransferases (PRMT) and lysine methyltransferases (PKMT).
Functional Roles: Regulatory roles in cellular processes like gene transcription and signal transduction.

Definition: Attachment of small ubiquitin-like modifiers (SUMOs) to proteins.
Significance: Involved in various processes like signaling, protein stability, and apoptosis.

Definition: Irreversible modification converting arginine into citrulline, influenced by protein arginine deiminases (PADs).
Clinical Relevance: Associated with diseases like rheumatoid arthritis and multiple sclerosis.

Modification Type	Mechanism
Protein Phosphorylation	Addition of a phosphate group to an amino acid residue.
Protein Glycosylation	Covalent addition of a carbohydrate moiety to an amino acid, forming a glycoprotein.
Protein Ubiquitination	Binding of a ubiquitin protein to a protein via a three-step process.
Protein Methylation	Addition of a methyl group, most often at lysine or arginine residues.
Protein Acetylation	Addition of an acetyl group to the N-terminus of a protein, or at lysine residues.

Takeaway: Post-translational modifications are crucial for protein functionality, stability, and regulation within biological systems; they hold significant implications in health and disease.