BIO101: 7B

1. How do cells know where to send proteins?

  • Protein sorting: The process of directing newly made proteins to their correct locations in or outside the cell.

  • Signal sequences: Specific sequences of amino acids that act like a “ZIP code” for a protein.

    • Usually about 15–60 amino acids long in the lecture slides.

    • Tell the cell where a protein needs to go.

    • Different destinations require different signals.

Examples:

  • Nuclear localization signal → nucleus

  • ER signal sequence → endoplasmic reticulum (ER)

  • Transit sequence → mitochondria or chloroplasts

Important: All protein synthesis begins on free ribosomes in the cytoplasm. What happens next depends on the protein's destination.

2. Cotranslational vs. post-translational transport

Cotranslational transport

  • The protein enters the ER while it is still being made.

  • The ribosome attaches to the ER.

  • Proteins usually destined for secretion, membranes, or the endomembrane system use this pathway.

    Post-translational transport

  • The protein is completely made before transport.

  • It is synthesized on free ribosomes and then sent to its destination.

  • Used for proteins destined for the cytosol, nucleus, mitochondria, chloroplasts, and peroxisomes.

Memory trick:

  • Co = together: Translation and transport happen together.

  • Post = after: Translation finishes before transport begins.

Feature

Cotranslational

Post-translational

When?

During synthesis

After synthesis

Ribosome

Attaches to ER

Remains free

Typical destinations

ER, Golgi, secretion, membranes

Cytosol, nucleus, mitochondria, chloroplasts

3. Transport into the nucleus

  • Proteins needed in the nucleus are made in the cytoplasm.

  • They enter through nuclear pore complexes, which control passage through the nuclear envelope.

  • A nuclear localization signal (NLS) identifies proteins that need to enter the nucleus.

  • A nuclear import receptor recognizes the signal and helps transport the protein.

  • Proteins can remain folded during nuclear import.

  • Nuclear transport requires energy.

  • Nuclear pores also allow mRNA to leave the nucleus and nucleotides to enter.

Remember: Nuclear import is post-translational, and proteins pass through nuclear pores rather than crossing the nuclear membrane directly.

4. Transport into mitochondria and chloroplasts

  • Most proteins in mitochondria and chloroplasts are made on free ribosomes in the cytoplasm.

  • These proteins are transported into the organelle after synthesis.

  • Chaperones keep the proteins unfolded so they can pass through membrane channels.

  • A signal sequence binds to a receptor on the organelle's outer membrane.

  • The protein passes through transport channels using energy from ATP.

  • Once inside, the protein folds into its functional shape.

  • The targeting signal may be removed by a signal peptidase.

Important transport complexes:

  • TOM/TIM: Transport proteins across the outer and inner mitochondrial membranes.

  • TOC/TIC: Transport proteins across the outer and inner chloroplast membranes.

Remember: These proteins generally need to be unfolded to pass through the channels.

5. The endomembrane system: ER → Golgi → destination

The endomembrane system includes the ER, Golgi apparatus, lysosomes, secretory vesicles, nuclear envelope, and plasma membrane.

Know this pathway in order:

1. Rough ER (RER)

Protein enters the ER during translation.

2. Protein processing

Protein folds and may receive carbohydrate groups.

3. Transport vesicle

Carries the protein from the ER to the Golgi.

4. Golgi apparatus

Further modifies, sorts, and packages proteins.

5. Final destination

Plasma membrane, secretion, lysosome, or another compartment.

Rough ER (RER)

  • Has ribosomes attached to its surface.

  • Produces proteins that enter the endomembrane system or leave the cell.

  • Soluble proteins enter the ER lumen.

  • Integral membrane proteins become embedded in the ER membrane during synthesis.

Signal recognition particle (SRP)

The SRP helps direct proteins to the ER.

  1. A protein begins to be made on a free ribosome.

  2. The ER signal sequence emerges from the ribosome.

  3. SRP binds the signal sequence and temporarily pauses translation.

  4. SRP brings the ribosome to the ER membrane.

  5. The ribosome attaches to a channel called the translocon.

  6. Translation resumes, and the growing protein enters the ER.

  7. The signal sequence may be removed, and the finished protein is released into the ER lumen.

Key terms:

  • SRP: Recognizes the ER signal sequence and directs the ribosome to the ER.

  • Translocon: Protein channel that allows a polypeptide to pass through the ER membrane.

  • Signal peptidase: Enzyme that cleaves the ER signal sequence.

Golgi apparatus

  • Receives proteins at the cis face.

  • Modifies, sorts, and packages proteins.

  • Sends proteins out from the trans face.

  • Uses transport vesicles to deliver proteins to their destinations.

Memory trick: Cis = comes in; trans = travels out.

6. Protein modification and folding

Glycosylation

  • Glycosylation is the addition of carbohydrate groups to proteins.

  • Proteins with attached carbohydrates are called glycoproteins.

  • Initial glycosylation occurs in the ER.

  • Further carbohydrate processing can occur in the Golgi.

  • Glycosylation helps prepare proteins for their destinations.

Protein folding

  • Newly made proteins must fold into the correct three-dimensional shape to function properly.

  • Chaperones help proteins fold and prevent them from clumping together.

  • Some proteins form disulfide bonds as they fold.

  • Incorrectly folded proteins may be identified and destroyed.

Important ER quality-control terms from the textbook:

  • BiP: An ER chaperone that helps proteins fold correctly.

  • Unfolded protein response (UPR): Responds to the buildup of misfolded proteins in the ER.

  • ER-associated degradation (ERAD): Sends misfolded proteins out of the ER to be degraded.

Post-translational modifications

Changes made to proteins after or during their synthesis can include:

  • Removing signal sequences or other amino acid segments.

  • Adding carbohydrate groups (glycosylation).

  • Phosphorylation, methylation, or acetylation.

  • Forming disulfide bonds.

  • Joining multiple polypeptide chains.

Example: Insulin

  1. Preproinsulin is produced.

  2. The signal segment is removed to form proinsulin.

  3. Disulfide bonds form between the future A and B chains.

  4. The intervening segment is removed, producing mature insulin.

7. Transport vesicles and membrane orientation

  • Transport vesicles carry soluble proteins, membrane lipids, and membrane proteins between compartments.

  • Vesicles form by budding from one membrane and fuse with another.

  • Vesicular transport moves materials both outward and inward through the endomembrane system.

  • Membrane orientation is maintained during transport:

    • The side facing the cytosol stays cytosol-facing.

    • The side facing the ER or vesicle lumen eventually faces the outside of the cell when the vesicle fuses with the plasma membrane.

This is especially important for understanding how membrane proteins end up with the correct parts facing inside or outside the cell.

8. Constitutive vs. regulated secretion

There are two major secretory pathways.

Constitutive secretion

Regulated secretion

Occurs continuously

Occurs when an appropriate signal is received

Vesicles move to and fuse with the plasma membrane

Materials are stored in secretory vesicles until needed

Supplies membrane components and releases proteins

Releases products at specific times

Remember: Constitutive = continuous; regulated = signal required.

9. Lysosomes and recycling materials

Lysosomes contain enzymes that break down materials so the cell can recycle their components.

The lecture covers three ways materials reach lysosomes:

  • Receptor-mediated endocytosis: Specific substances bind receptors and are brought into the cell in vesicles.

  • Phagocytosis: The cell engulfs large particles or other material.

  • Autophagy: The cell breaks down its own damaged or unneeded components.

10. GFP and identifying protein locations

The textbook also describes a technique for finding where a protein is located in living cells.

  • Green fluorescent protein (GFP) can be attached to a protein of interest.

  • The resulting protein is called a GFP fusion protein.

  • Scientists introduce the appropriate DNA into cells, which then produce the tagged protein.

  • Fluorescence microscopy reveals where the protein is located.

  • Different fluorescent protein variants can help researchers track multiple proteins.

One limitation: the fluorescent tag can interfere with protein function, so researchers should test whether the fusion protein still works normally.