Unit 5: Protein Distribution and Transport

Unit 5: Protein Distribution and Transport

• Protein synthesis is the final stage of gene expression
• Protein synthesis involves translation of mRNA, folding, and processing.
• Gene expression is regulated at the translational level
• Different mechanisms modify protein quantity and activity (e.g., degradation)

Index 5.1 Protein synthesis, processing and regulation:

• mRNA translation
• Protein folding and processing
• Regulation of protein function
• Protein degradation

Index 5.2 Endoplasmic reticulum:

• Membrane-bound network of tubules and sacs
• Continuous membrane
• Roughly 50% of all cell membranes
• Rough ER is associated with ribosomes, involved in protein synthesis and processing.
• Smooth ER does not associate with ribosomes, involved in lipid metabolism

Index 5.3 Golgi apparatus:

• Proteins synthesized and processed in the ER are reprocessed and distributed (e.g., lysosomes, plasma membrane, secretion)
• Glycolipids and sphingomyelin are synthesized in the Golgi
• Complex processing and distribution
• Multi-compartment structure functions in protein modifications
• Involved in secretion, sorting, modifications

Index 5.4 Vesicle transport mechanism:

• Fundamental cellular activity
• Responsible for traffic between membrane-bound compartments
• Key for functional organization of the cell
• Vesicle transport involves selective packaging and recognition of target membrane
• Mechanisms controlling vesicle packing, budding, distribution, and fusion are areas of extensive research

Index 5.5 Lysosomes

• Membrane-bound organelles containing enzymes to degrade biological polymers
• Lysosomes are a crucial part of the cell's digestive system
• They degrade material taken up from outside the cell and digest cellular waste
• Dense spherical vacuoles of varying sizes and shapes

Protein Folding and Processing

• Polypeptides fold into 3D conformations
• Many proteins aggregate into functional complexes
• Post-translational modifications include cleavage, covalent union of carbohydrates and lipids
• Necessary for correct cellular function and localization
• Chaperones facilitate folding of other proteins or assembly processes of protein complexes
• Essential in preventing misfolding and aggregation
• Examples of essential chaperones include Hsp70, chaperonins.

Diseases due to protein folding defects

• Protein aggregation results in a variety of diseases, such as Alzheimer's, Parkinson's and others
• Characterized by accumulation of misfolded proteins

Regulation of protein function via small molecules

• Most enzymes are regulated by modifications in their conformation
• Often mediated by non-covalent binding to small molecules
• Allosteric regulation involves a change in conformation and enzyme activity outside of the active site
• Retroinhibition of metabolic pathways
• Regulation of translation factors (e.g., eEF-1a) through GTP and GDP binding

Phosphorylation and other protein modifications

• Phosphorylation is the most common covalent modification, regulating protein activity
• Protein kinases transfer phosphate groups from ATP to side chains of serine, threonine, or tyrosine
• Protein phosphorylation is reversed by phosphatases that catalyze hydrolysis of phosphorylated amino acids

Other modifications by covalent bonding (e.g.)

• Acetylation
• Methylation
• Nitrosylation
• Glycosylation

Glycosylation

• Addition of carbohydrate chains to proteins to form glycoproteins
• More frequent in eukaryotic cells
• Proteins folding, intracellular targeting, and recognition in intercellular interactions. Examples: N-linked and O-linked glycoproteins.

Protein-protein interactions

• Many proteins are multi-unit, involving interactions between subunits that regulate activity
• For example, cAMP-dependent kinases

Protein Degradation

• The quantity of proteins in the cell is regulated by their rate of synthesis and degradation
• The half-life of proteins varies, ranging from a few minutes to several days.
• Pathways involve ubiquitin-proteasome (degradation of proteins targeted by tags like ubiquitin) and lysosomal proteolysis.

Quality control in the ER

• Misfolded proteins are removed from the ER through ER-associated degradation (ERAD).
• Chaperones and protein-processing enzymes act as sensors detecting misfolding

Export (secretory pathway)

• Proteins and lipids are exported from the endoplasmic reticulum (ER) via vesicles
• Different types of transport vesicles are used to transport the materials to the Golgi

The Golgi Apparatus

• Primarily involved in the processing and distribution of proteins and other molecules
• The Golgi's structure divides into distinct regions including cis, medial, and trans, with further modification at the trans-Golgi network
• N-glycosylation is a key modification

Labeling of proteins to target the ER

• Proteins can be directed to the ER via co- and post-translational translocation
• A signal sequence is a key element in the directing process
• The signal sequence contains between 15-40 amino acids, often including basic amino acids and a hydrophobic segment, leading to proper targeting for the ER

Translocation of proteins into the ER membrane

• Multiple mechanisms handle the translocation of proteins into ER membrane

Lipid Binding and Lipid Synthesis

• Lipids are hydrophobic molecules
• Synthesized in the smooth endoplasmic reticulum (SER)
• Phospholipids are important membrane components, derived from glycerol
• The SER is involved in the synthesis of other membrane lipids (cholesterol and ceramide)

Synthesis of phospholipids

• Fatty acids are transferred to glycerol-3-phosphate (creating phosphatidic acid).
• Phospholipids are synthesized on the cytoplasmic side of the ER

Translocation of phospholipids across the ER membrane

• Enzymes facilitate translocation through the membrane
• Phospholipid flippases cause uniform growth of two halves of the phospholipid bilayer

Insertion of proteins into the ER membrane

• Integral membrane proteins are embedded in the membrane by hydrophobic regions that cross the lipid membrane.
• Proteins that cross the membrane often have a series of amino-acid regions with alpha-helices
• The orientation of protein insertion is important, with some proteins having the amino or carboxyl end exposed on one side (e.g., cytosolic side).

The Ubiquitin-Proteasome Pathway and Lysosomal Proteins

• Proteins destined for lysosomes are recognized and processed differently during their passage through the Golgi
• Modification of these proteins involve phosphorylation of mannose residues to distinguish them from the secretory pathway
• Ubiquitin-proteasome system, and lysosomal acid hydrolases help maintain the correct pH

Endocytosis and Lysosome Formation

• One main function of lysosomes is the degradation of material captured by cell externalization through endocytosis
• Endosomes are the result of vesicles fusing with membrane material.

Phagocytosis and Autophagy

• Lysosomes digest material via these pathways
• Phagocytosis, specialized cells ingest and degrade large particles
• Autophagy is a cell's own components replacement function

Gaucher's Disease

• Lysosomal storage disease due to a deficiency in glucocerebrosidase enzymes
• Accumulation of undigested materials in lysosomes, leading to cellular dysfunction and health issues.
• Several clinical types with varying severities

Explore the critical concepts surrounding protein synthesis, processing, and regulation in biological systems. This quiz covers mRNA translation, the role of the endoplasmic reticulum, and the functions of the Golgi apparatus. Test your understanding of how these cellular components work together to ensure proper protein distribution and activity.